Methods and compositions for targeting rna polymerases and non-coding rna biogenesis to specific loci

ABSTRACT

The present disclosure relates to the use of recombinant proteins for inducing epigenetic modifications at specific loci, as well as to methods of using these recombinant proteins for reducing the expression of genes in plants.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/342,814, filed on May 27, 2016, and U.S. Provisional Application No.62/450,504, filed on Jan. 25, 2017, the disclosures of which areincorporated herein by reference in their entirety.

SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file isincorporated herein by reference in its entirety: a computer readableform (CRF) of the Sequence Listing (file name: 262232001140SEQLIST.txt,date recorded: May 26, 2017, size: 3,490 KB).

FIELD

The present disclosure relates to the use of recombinant proteins forinducing epigenetic modifications at specific loci, as well as tomethods of using these recombinant proteins for reducing the expressionof genes in plants.

BACKGROUND

Epigenetic marks are enzyme-mediated chemical modifications of DNA andof its associated chromatin proteins. Although epigenetic marks do notalter the primary sequence of DNA, they do contain heritable informationand play key roles in regulating genome function. Such modifications,including cytosine methylation, posttranslational modifications ofhistone tails and the histone core, and the positioning of nucleosomes(histone octamers wrapped with DNA), influence the transcriptional stateand other functional aspects of chromatin. For example, methylation ofDNA and certain residues on the histone H3N-terminal tail, such as H3lysine 9 (H3K9), are important for transcriptional gene silencing andthe formation of heterochromatin. Such marks are essential for thesilencing of nongenic sequences, including transposons, pseudogenes,repetitive sequences, and integrated viruses, that become deleterious tocells if expressed and hence activated. Epigenetic gene silencing isalso important in developmental phenomena such as imprinting in bothplants and mammals, as well as in cell differentiation andreprogramming. Having the ability to specifically control target genesilencing is thus of great interest.

Different pathways involved in epigenetic silencing have been previouslydescribed, and include histone deacetylation, H3K27 and H3K9methylation, H3K4 demethylation, and DNA methylation of promoters. Anavenue to achieve DNA methylation is via a phenomenon known asRNA-directed DNA methylation, where non-coding RNAs act to directmethylation of a DNA sequence. In plants, proteins generally do not linkthe recognition of a specific DNA sequence with the establishment of anepigenetic state. Thus, endogenous plant epigenetic regulators generallycannot be used for epigenetic silencing of specific genes or transgenesin plants.

Accordingly, a need exists for improved epigenetic regulators that arecapable of being targeted to specific loci to induce epigenetic genesilencing activity in plants.

BRIEF SUMMARY

The present disclosure relates to a method for reducing expression ofone or more target nucleic acids in a plant, the method including: (a)providing a plant including a recombinant nucleic acid encoding arecombinant polypeptide including a nuclease-deficient CAS9 polypeptide(dCAS9) or fragment thereof and a polypeptide selected from an SHH1polypeptide or fragment thereof, an SHH2 polypeptide or fragmentthereof, an AGO4 polypeptide or fragment thereof, an HDA6 polypeptide orfragment thereof, an NRPD1 polypeptide or fragment thereof, an NRPE1polypeptide or fragment thereof, a JMJ14 polypeptide or fragmentthereof, an RDR2 polypeptide or fragment thereof, an NRPD2A/NRPE2polypeptide or fragment thereof, an NRPB3/NRPD3/NRPE3A polypeptide orfragment thereof, an NRPE3B polypeptide or fragment thereof, anNRPB11/NRPD11/NRPE11 polypeptide or fragment thereof, anNRPB10/NRPD10/NRPE10 polypeptide or fragment thereof, anNRPB12/NRPD12/NRPE12 polypeptide or fragment thereof, anNRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof; and a crRNA and tracrRNA, or fusionsthereof; and (b) growing the plant under conditions where therecombinant nucleic acid is expressed and where the recombinantpolypeptide is targeted to the one or more target nucleic acids, therebyreducing expression of the one or more target nucleic acids. In someembodiments, the recombinant polypeptide interacts with an RNApolymerase. In some embodiments, the RNA polymerase is RNA polymerase IVor RNA polymerase V. In some embodiments that may be combined with anyof the preceding embodiments, the recombinant polypeptide inducesRNA-directed DNA methylation. In some embodiments that may be combinedwith any of the preceding embodiments, the one or more target nucleicacids are endogenous nucleic acids. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are heterologous nucleic acids. In some embodiments thatmay be combined with any of the preceding embodiments, expression of theone or more target nucleic acids is silenced.

The present disclosure also relates to a recombinant nucleic acid whichencodes a recombinant polypeptide including a nuclease-deficient CAS9polypeptide (dCAS9) or fragment thereof and a polypeptide selected froman SHH1 polypeptide or fragment thereof, an SHH2 polypeptide or fragmentthereof, an AGO4 polypeptide or fragment thereof, an HDA6 polypeptide orfragment thereof, an NRPD1 polypeptide or fragment thereof, an NRPE1polypeptide or fragment thereof, a JMJ14 polypeptide or fragmentthereof, an RDR2 polypeptide or fragment thereof, an NRPD2A/NRPE2polypeptide or fragment thereof, an NRPB3/NRPD3/NRPE3A polypeptide orfragment thereof, an NRPE3B polypeptide or fragment thereof, anNRPB11/NRPD11/NRPE11 polypeptide or fragment thereof, anNRPB10/NRPD10/NRPE10 polypeptide or fragment thereof, anNRPB12/NRPD12/NRPE12 polypeptide or fragment thereof, anNRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof. The present disclosure furtherrelates to expression vectors including the recombinant nucleic acid ofthe preceding embodiment, and a host cell including the expressionvector of the preceding embodiment. In some embodiments, the host cellis a plant cell. The present disclosure also relates to a recombinantplant including the recombinant nucleic acids of the precedingembodiments.

Other aspects of the present disclosure relate to a plant having reducedexpression of one or more target nucleic acids according to the methodof any one of the preceding embodiments, as well as a progeny plant ofthe plant of the preceding embodiment. In some embodiments, the progenyplant has reduced expression of the one or more target nucleic acids anddoes not include the recombinant nucleic acid.

The present disclosure also relates to a method for reducing expressionof one or more target nucleic acids in a plant, the method including:(a) providing a plant including: a recombinant nucleic acid encoding arecombinant polypeptide selected from an SHH1-like protein, an SHH2-likeprotein, an AGO4-like protein, an HDA6-like protein, an NRPD1-likeprotein, an NRPE1-like protein, a JMJ14-like protein, an RDR2-likeprotein, an NRPD2A/NRPE2-like protein, an NRPB3/NRPD3/NRPE3A-likeprotein, an NRPE3B-like protein, an NRPB11/NRPD11/NRPE11-like protein,an NRPB10/NRPD10/NRPE10-like protein, an NRPB12/NRPD12/NRPE12-likeprotein, an NRPB6A/NRPD6A/NRPE6A-like protein, anNRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-like protein, anNRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, an SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein; and a crRNA and tracrRNA, or fusions thereof,and where the plant expresses a dCAS9 protein; and (b) growing the plantunder conditions where the recombinant nucleic acid is expressed andwhere the recombinant polypeptide is targeted to the one or more targetnucleic acids, thereby reducing expression of the one or more targetnucleic acids. In some embodiments, the recombinant polypeptide includesa dCAS9 protein or fragment thereof. In some embodiments, therecombinant polypeptide includes an MS2 coat protein or fragmentthereof. In some embodiments, the recombinant polypeptide includes anscFV antibody or fragment thereof. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments, theRNA polymerase is RNA polymerase IV or RNA polymerase V. In someembodiments that may be combined with any of the preceding embodiments,the recombinant polypeptide induces RNA-directed DNA methylation. Insome embodiments that may be combined with any of the precedingembodiments, the one or more target nucleic acids are endogenous nucleicacids. In some embodiments that may be combined with any of thepreceding embodiments, the one or more target nucleic acids areheterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, expression of the one or moretarget nucleic acids is silenced.

The present disclosure also relates to a recombinant nucleic acid whichencodes a recombinant polypeptide selected from an SHH1-like protein, anSHH2-like protein, an AGO4-like protein, an HDA6-like protein, anNRPD1-like protein, an NRPE1-like protein, a JMJ14-like protein, anRDR2-like protein, an NRPD2A/NRPE2-like protein, anNRPB3/NRPD3/NRPE3A-like protein, an NRPE3B-like protein, anNRPB11/NRPD11/NRPE11-like protein, an NRPB10/NRPD10/NRPE10-like protein,an NRPB12/NRPD12/NRPE12-like protein, an NRPB6A/NRPD6A/NRPE6A-likeprotein, an NRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-likeprotein, an NRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein. The present disclosure further relates toexpression vectors including the recombinant nucleic acid of thepreceding embodiment, and a host cell including the expression vector ofthe preceding embodiment. In some embodiments, the host cell is a plantcell. The present disclosure also relates to a recombinant plantincluding the recombinant nucleic acids of the preceding embodiments.

Other aspects of the present disclosure relate to a plant having reducedexpression of one or more target nucleic acids according to the methodof any one of the preceding embodiments, as well as a progeny plant ofthe plant of the preceding embodiment. In some embodiments, the progenyplant has reduced expression of the one or more target nucleic acids anddoes not include the recombinant nucleic acid.

The present disclosure also relates to a method for reducing expressionof one or more target nucleic acids in a plant, including: (a) providinga plant including a recombinant nucleic acid, where the recombinantnucleic acid encodes a recombinant polypeptide including a first aminoacid sequence including a DNA-binding domain and a second amino acidsequence including a polypeptide selected from the group of an SHH1polypeptide or fragment thereof, an SHH2 polypeptide or fragmentthereof, an AGO4 polypeptide or fragment thereof, an HDA6 polypeptide orfragment thereof, an NRPD1 polypeptide or fragment thereof, an NRPE1polypeptide or fragment thereof, a JMJ14 polypeptide or fragmentthereof, an RDR2 polypeptide or fragment thereof, an NRPD2A/NRPE2polypeptide or fragment thereof, an NRPB3/NRPD3/NRPE3A polypeptide orfragment thereof, an NRPE3B polypeptide or fragment thereof, anNRPB11/NRPD11/NRPE11 polypeptide or fragment thereof, anNRPB10/NRPD10/NRPE10 polypeptide or fragment thereof, anNRPB12/NRPD12/NRPE12 polypeptide or fragment thereof, anNRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof; and (b) growing the plant underconditions where the recombinant polypeptide encoded by the recombinantnucleic acid is expressed and binds to the one or more target nucleicacids, thereby reducing expression of the one or more target nucleicacids. In some embodiments, the DNA-binding domain includes a zincfinger domain. In some embodiments, the zinc finger domain includes two,three, four, five, six, seven, eight, or nine zinc fingers. In someembodiments, the zinc finger domain is a zinc finger array. In someembodiments, the zinc finger domain is selected from the group of aCys2His2 (C2H2) zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments, the DNA-binding domain is selected from the groupof a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments, theDNA-binding domain includes a TAL effector targeting domain. In someembodiments, the DNA-binding domain includes three C2H2 zinc fingerdomains. In some embodiments, the recombinant polypeptide interacts withan RNA polymerase. In some embodiments, the RNA polymerase is RNApolymerase IV or RNA polymerase V. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide induces RNA-directed DNA methylation. In some embodimentsthat may be combined with any of the preceding embodiments, the one ormore target nucleic acids are endogenous nucleic acids. In someembodiments that may be combined with any of the preceding embodiments,the one or more target nucleic acids are heterologous nucleic acids. Insome embodiments that may be combined with any of the precedingembodiments, expression of the one or more target nucleic acids issilenced.

In another aspect, the present disclosure provides a method for reducingexpression of one or more target nucleic acids in a plant, including:(a) providing a plant including a recombinant polypeptide selected froman SHH1-like protein, an SHH2-like protein, an AGO4-like protein, anHDA6-like protein, an NRPD1-like protein, a JMJ14-like protein, anRDR2-like protein, an NRPD2A/NRPE2-like protein, anNRPB3/NRPD3/NRPE3A-like protein, an NRPE3B-like protein, anNRPB11/NRPD11/NRPE11-like protein, an NRPB10/NRPD10/NRPE10-like protein,an NRPB12/NRPD12/NRPE12-like protein, an NRPB6A/NRPD6A/NRPE6A-likeprotein, an NRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-likeprotein, an NRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein; and (b) growing the plant under conditionswhereby the recombinant polypeptide is targeted to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids.

In another aspect, the present disclosure provides a method for reducingexpression of one or more target nucleic acids in a plant, including:(a) providing a plant including: a first recombinant polypeptideincluding a nuclease-deficient CAS9 polypeptide (dCAS9) or fragmentthereof and a multimerized epitope; a second recombinant polypeptideincluding a DRM2-MTase polypeptide or a DNMT3A-DNMT3L fusionpolypeptide, and an affinity polypeptide that specifically binds to theepitope; a crRNA and a tracrRNA, or fusions thereof; and (b) growing theplant under conditions whereby the first and second recombinantpolypeptides are targeted to the one or more target nucleic acids,thereby reducing expression of the one or more target nucleic acids.

In another aspect, the present disclosure provides a recombinant vectorincluding: a first nucleic acid sequence including a plant promoter andthat encodes a recombinant polypeptide including a nuclease-deficientCAS9 polypeptide (dCAS9) or fragment thereof and a multimerized epitope;a second nucleic acid sequence including a plant promoter and thatencodes a recombinant polypeptide including a DRM2-MTase polypeptide ora DNMT3A-DNMT3L fusion polypeptide, and an affinity polypeptide thatspecifically binds to the epitope; and a third nucleic acid sequenceincluding a promoter and that encodes a crRNA and a tracrRNA, or fusionsthereof. Also provided are host cells including the vector of thepreceding embodiment, and a recombinant plant including the vector ofthe preceding embodiment.

In another aspect, the present disclosure provides a plant havingreduced expression of one or more target nucleic acids as a consequenceof the method of any of the preceding embodiments. Also provided is aprogeny plant of the plant of the preceding embodiment. In someembodiments, the progeny plant has reduced expression of the one or moretarget nucleic acids and does not include the recombinant polypeptidetargeted to the one or more target nucleic acids.

DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawings will be provided by the office upon request and paymentof the necessary fee.

FIG. 1A and FIG. 1B illustrate an alignment of AGO4 and related proteinsfrom A. thaliana.

FIG. 2 illustrates an alignment of HDA6 and related proteins from A.thaliana.

FIG. 3A and FIG. 3B illustrate an alignment of JMJ14 and relatedproteins from A. thaliana.

FIG. 4A and FIG. 4B illustrate an alignment of RDR2 and related proteinsfrom A. thaliana.

FIG. 5 illustrates bisulfite sequencing results of an exemplary NRPD1-ZFtransgenic line in an fwa-4 mutant background that exhibited earlyflowering.

FIG. 6 illustrates bisulfite sequencing results of exemplary AGO4-ZF,HDA6-ZF, JMJ14-ZF, NRPD2-ZF, RDR2-ZF, SHH2-ZF, SUVR2-ZF, and DMS3-ZFtransgenic lines in an fwa-4 mutant background that exhibited earlyflowering.

FIG. 7A illustrates the structure of an exemplary fusion constructcontaining an epigenetic regulator C-terminally fused to a dCAS9protein. FIG. 7B illustrates the structure of an exemplary fusionconstruct containing an epigenetic regulator N-terminally fused to adCAS9 protein.

FIG. 8A illustrates the structure of an exemplary fusion constructcontaining an epigenetic regulator C-terminally fused to a dCAS9protein. FIG. 8B illustrates the structure of an exemplary fusionconstruct containing an epigenetic regulator N-terminally fused to adCAS9 protein.

FIG. 9 illustrates the structure of exemplary fusion constructs used ina modified CRISPR-targeting scheme involving the use of MS2 proteins.

FIG. 10 illustrates the structure of exemplary fusion constructs used ina modified CRISPR-targeting scheme involving the use of SunTagconstructs.

FIG. 11 illustrates BS-PCR of the FWA promoter in agroinfiltrated leavescarrying the specified constructs 3 days post infiltration (dpi).

FIG. 12 illustrates relative expression of FWA-driven Luciferase inagroinfiltrated leaves carrying the specified constructs 3 days postinfiltration, measured by real-time qPCR. Error bars=Standard error.

FIG. 13 illustrates methylation profiles of a wild-type Col-O plantcompared to two fwa-4 plants that have been transformed withZN-DRM2-MTase constructs. The promoter region of FWA is framed in red.

FIG. 14A illustrates a schematic of the ATRX-ZF expression cassette.FIG. 14B illustrates flowering time data for wild-type Col-O, fwamutants, and two independent ATRX-ZF T2 lines (A19 and A21). N=32-50plants for each plant line presented.

FIG. 15 illustrates methylation profiles at the FWA promoter region forwild-type Col-O, fwa-4 mutant, and two plants each from threeindependent ATRX-ZF T2 lines (A6, A19, and A21).

FIG. 16A illustrates a schematic of the MOM1-ZF expression cassette.FIG. 16B illustrates flowering time data for wild-type Col-O, fwa-4mutant, and four independent MOM1-ZF T2 lines (M1, M2, M3, and M4). N=50plants for each plant line presented.

FIG. 17 illustrates methylation profiles at the FWA promoter region forwild-type Col-O, fwa-4 mutant, and two plants each from threeindependent MOM1-ZF T2 lines (M1, M2, and M3). Line M2-2 is derived froma T1 line housing MOM-ZF, but M2-1 is a T2 plant that does not carry theMOM1-ZF transgene.

FIG. 18 illustrates flowering time of wild-type Col-O plants, fwa-4mutant plants, and fwa-4 T1 plants transformed with ZF_SssI. Plants weregrown on soil under long day photoperiods until the plants flowered, atwhich time flowering time was assessed.

FIG. 19 illustrates whole genome bisulfite sequencing results of T1ZF_SssI and Col-O wild-type plants. DNA methylation of two independenttransgenic lines that showed an early flowering phenotype was analysedby BS-seq. Methylation at different contexts (CG, CHG and CHH, where His C, T, or A) is shown for a wild-type Col-O plant and a representativeZF108-SssI line in which ZF108-SssI was transformed into theunmethylated fwa-4 epimutant. The FWA promoter is marked in red.

FIG. 20 illustrates a genomic zoom-out of the whole genome bisulfitesequencing results presented in FIG. 19 for T1 ZF_SssI and Col-Owild-type plants. DNA methylation of two independent transgenic linesthat showed an early flowering phenotype was analysed by BS-seq.Methylation at different contexts (CG, CHG and CHH, where H is C, T, orA) is shown for a wild-type Col-O plant and a representative ZF108-SssIline in which ZF108-SssI was transformed into the unmethylated fwaepimutant. The FWA promoter is marked in red.

FIG. 21A and FIG. 21B illustrate the phenotypes of ZF108-SssI T2 plants.Plants from some of the ZF108-SssI T2 lines displayed abnormaldevelopment and formed chimeras where different sectors of the sameleaves displayed chlorosis.

FIG. 22 illustrates a schematic of the expression cassettes present inthe vector housing the SunTag DRM2-MTase expression system.

FIG. 23 illustrates fluorescence microscopy of T2 A. thaliana plants(fwa-4) transformed with the iteration of the SunTag DRM2-MTase vectorwhere DRM2-MTase was fused to an SV40-type NLS. Tissue shown is midveintissue.

FIG. 24 illustrates SunTag-DRM2-MTase induction of DNA methylation ofthe FWA promoter. Results are from whole genome bisulfite sequencingfrom the unmethylated fwa epiallele (top row) and six different T2plants containing the SunTag-DRM2-MTase system with gRNA4 targeted toFWA. Shown are CHH methylation tracks for four independent plants fromtransgenic line 1 and two independent plants from transgenic line 3.Bottom row shows signal from chromatin immunoprecipitation sequencing ofdCas9 in a T2 SunTag+gRNA4 line. The methylation is highly localized tothe region of the FWA promoter targeted by dCas9.

FIG. 25 illustrates SunTag-DRM2-MTase induction of DNA methylation at agenomic off-target. Results are from whole genome bisulfite sequencingfrom the unmethylated fwa epiallele (top row) and six different T2plants containing the SunTag-DRM2-MTase system with gRNA4. Shown are CHHmethylation tracks for four independent plants from transgenic line 1and two independent plants from transgenic line 3. Bottom row showssignal from chromatin immunoprecipitation sequencing of dCas9 of a T2SunTag+gRNA4 line. The methylation is highly localized at the regiontargeted by dCas9.

FIG. 26 illustrates McrBC PCR of samples expressing an artificial zincfinger fused to DRM2-Mtase (ZF_DRM2-MTase) designed to target thepromoter of SUPERMAN gene. Blue bars represent the ratio of Digested vsNon-digested DNA samples from 3 independent T1 transgenic plantsexpressing the SUP-7F1_DRM2-MTase, or 4 different transgenic linesexpressing the SUP-ZF3_DRM2-MTase, together with a wild type Col0control using oligos specific for the SUPERMAN promoter. Red barsrepresent the ratio of Digested vs Non-digested of the same samplesusing oligos specific for a control region, not targeted by the fusionprotein.

FIG. 27 illustrates whole genome bisulfite sequencing analysis.Screenshot of the region including the SUPERMAN gene showing methylationin different contexts (CG, CHG and CHH, where H is C, T or A) of Col0wild type control plants, one line expressing SUP-ZF1_DRM2-MTase and oneline expressing SUP-ZF3_DRM2-MTase. SUP-ZF1 and SUP-ZF3 Zinc Fingersbind to an overlapping sequence, with SUP-ZF1 targeted to an 18 basepair sequence and SUP-ZF3 targeted to a 15 base pair sequence. TheSUP-ZF11 binding site is indicated with a pink square under the SUPERMANpromoter.

FIG. 28 illustrates a screenshot of the FWA region showing methylationlevels of different lines expressing ZF108 fused to various proteins,along with control lines (Col0 and fwa-4). Different tracks indicatedifferent cytosine methylation context (CG, CHG and CHH, where H is C, Aor T). ZF108 Chromatin Immunoprecipitation (ChIP) indicates the specificlocation of ZF108 binding to the FWA promoter.

FIG. 29 illustrates a screenshot at a ZF108-related locus showingmethylation levels of different lines expressing ZF108 fused to variousproteins, along with control lines (Col0 and fwa-4). Different tracksindicate different cytosine methylation context (CG, CHG and CHH, whereH is C, A or T). ZF108 Chromatin Immunoprecipitation (ChIP) indicatesthe specific location of ZF108 binding to a location near the At4g09510gene, which contains a DNA sequence which is very similar to thesequence targeted at FWA.

FIG. 30 illustrates screenshots showing ChIP-seq signals from ZF108-HAlines and ZF108-DMS3 lines in either the region of the designed zincfinger binding site (CGGAAAGATGTATGGGCT) in the FWA promoter (toppanel), or at a region on chromosome 4 containing two DNA sequenceswhich are very close in sequence to the designed ZF108 sequence (bottompanel). The FWA region contains two sequences that are identical to theZF108 binding sites. The additional region on chromosome 4 contains twosequences that contain 17 matches to the ZF108 binding site.

FIG. 31 illustrates flowering time of DMS3-ZF T1 plants. Flowering timeof T1 plants in fwa-4 or fwa-4 crossed with drm1/2 “drm12”. Wild type“Col0” and fwa-4 “fwa” controls were also measured. Flowering time of T1plants was scored as total number of leaves after flowering.

FIG. 32 illustrates flowering time of HDA6-ZF T1 plants. Flowering timeof T1 plants in fwa-4 or fwa-4 crossed with drm1/2 “drm12”. Wild type“Col0” and fwa-4 “fwa” controls were also measured. Flowering time of T1plants was scored as total number of leaves after flowering.

FIG. 33 illustrates flowering time of JMJ14-ZF T1 plants. Flowering timeof T1 plants in fwa-4 or fwa-4 crossed with drm1/2 “drm12”. Wild type“Col0” and fwa-4 “fwa” controls were also measured. Flowering time of T1plants was scored as total number of leaves after flowering.

FIG. 34 illustrates flowering time of SHH2-ZF T1 plants. Flowering timeof T1 plants in fwa-4 or fwa-4 crossed with drm1/2 “drm12”. Wild type“Col0” and fwa-4 “fwa” controls were also measured. Flowering time of T1plants was scored as total number of leaves after flowering.

FIG. 35 illustrates DNA methylation analysis of two early flowering T1plants in either fwa-4 or fwa-4 crossed with drm1/2 “drm12”, analyzed byBS-PCR. Methylation levels at 3 different regions of the FWA promoterand one control region, corresponding to a downstream gene, are shown.

FIG. 36 illustrates a screenshot of Whole-Genome Bisulfite Sequencingdata of the FWA promoter region for different lines expressing variousZF108 fusion proteins. Even though these plants displayed an earlyflowering phenotype indicative of FWA silencing, this data shows thatthese proteins are capable of causing silencing without inducing DNAmethylation of FWA.

FIG. 37 illustrates flowering time of T3 populations derived fromZF-SssI T2 plants (ZF-SssI transformed into the fwa-4 epimutant) thathad the ZF-SssI transgene (ZF+) or had segregated it away (ZF−). Col0and fwa-4 were used as controls for flowering time.

FIG. 38 illustrates a screenshot at the FWA locus of whole genomebisulfite sequencing data corresponding to T2 or T3 plants from a linethat expresses ZF108-SssI (ZF+) or where the transgene has beensegregated out (ZF—).

FIG. 39 illustrates a zoomed out view of the region presented in FIG.38. FWA promoter is indicated with an arrow.

FIG. 40 illustrates McrBC-PCR of Col0, fwa-4 and 7 independent T1transgenic lines expressing MBD9-ZF. qPCR was performed using oligosspecific for the FWA promoter or a control region. The ratio betweendigested and undigested samples is shown.

FIG. 41 illustrates amino acid alignment of the methyl-binding domain ofdifferent MBD proteins from Arabidopsis and humans. Red indicates highamino acid conservation while blue indicates low conservation. Proteinswere aligned using CLC Main Workbench software.

FIG. 42 illustrates whole-genome bisulfite sequencing data of T1 SunTagDRM2-MTase (DRM) Arabidopsis thaliana transgenic plants (Columbiabackground) with two sgRNAs driven by the U6 promoter targeting SUPERMAN(SUP). Shown in the figure are CHH methylation tracks of the Colcontrol, T1 SunTag DRM SUP line1, T1 SunTag DRM SUP line2, T1 SunTag DRMSUP line3, and T1 SunTag DRM SUP line4. SUPERMAN is annotated at the topof the tracks. Targeted methylation is present in SUPERMAN's promoterand extends through the transcriptional start site.

FIG. 43 illustrates whole-genome bisulfite sequencing data of T1 SunTagDRM2-MTase (DRM) Arabidopsis thaliana transgenic plants (Columbiabackground) with two sgRNAs driven by the U6 promoter targeting SUPERMAN(SUP). Shown in the figure are CHG methylation tracks of the Colcontrol, T1 SunTag DRM SUP line1, T1 SunTag DRM SUP line2, T1 SunTag DRMSUP line3, and T1 SunTag DRM SUP line4. SUPERMAN is annotated at the topof the tracks. Targeted methylation is present in SUPERMAN's promoterand extends through the transcriptional start site.

FIG. 44 illustrates qRT-PCR expression data of SUPERMAN in flowers of T1SunTag DRM SUP line1 plants as compared to the Col control. Transgenicplants show about a 2-fold downregulation of SUPERMAN transcriptsrelative to Col. Error bars indicate SEM of two replicates.

FIG. 45 illustrates whole-genome bisulfite sequencing data of T1 SunTagDNMT3A-3L Arabidopsis thaliana transgenic plants (fwa-4 background) withsgRNA #4 (g4) driven by the U6 promoter targeting FWA. Shown in thefigure are CG methylation tracks of the fwa-4 control, and two earlyflowering lines: T1 SunTag DNMT3A-3L g4 line2 and T1 SunTag DNMT3A-3L g4line3. Targeted methylation is present at the 5′ end of the gene.

DETAILED DESCRIPTION Overview

The following description is presented to enable a person of ordinaryskill in the art to make and use the various embodiments. Descriptionsof specific devices, techniques, methods, and applications are providedonly as examples. Various modifications to the examples described hereinwill be readily apparent to those of ordinary skill in the art, and thegeneral principles defined herein may be applied to other examples andapplications without departing from the spirit and scope of the variousembodiments. Thus, the various embodiments are not intended to belimited to the examples described herein and shown.

The present disclosure relates to the use of recombinant proteins forinducing epigenetic modifications at specific loci, as well as tomethods of using these recombinant proteins for reducing the expressionof genes in plants.

In Arabidopsis, establishment of all DNA methylation and maintenance ofmuch of the non-CG methylation involves the RNA-directed DNA methylation(RdDM) pathway (Aufsatz et al., 2002; Pelissier and Wassenegger, 2000).DNA methylation is first established by a protein called DRM2 and istargeted by 24 nt small interfering RNAs (siRNAs) through the RdDMpathway that involves two plant-specific RNA polymerases: RNA PolymeraseIV (Pol IV), which functions to initiate siRNA biogenesis; and RNAPolymerase V (Pol V), which functions in the downstream DNAmethyltransferase targeting phase of the RdDM pathway to generatenon-coding scaffold transcripts that recruit downstream RdDM factors.Thus, RNA-directed DNA methylation (RdDM) in Arabidopsis involves boththe synthesis of non-coding, small-interfering RNAs by Pol IV and thesynthesis of non-coding scaffold RNAs by Pol V.

Specifically, and without wishing to be bound by theory, it is believedthat there are two main steps in this pathway that are thought to targetthe DNA methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2(DRM2)(Cao and Jacobsen, 2002). The first upstream step involves thesynthesis of 24 nucleotide small interfering RNAs (siRNAs) by theconcerted actions of RNA POLYMERASE IV (Pol IV or NRPD), RNA-DIRECTEDRNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3)(Pontier et al., 2005).The second downstream step involves the production of scaffoldtranscripts by RNA POLYMERASE V (Pol V or NRPE) with the help of the DDRcomplex (DRD1, a SWI/SNF2 chromatin remodeler; DMS3, a chromosomalarchitectural protein; RDM1, unknown function). Without wishing to bebound by theory, it is then believed that ARGONAUTE 4 (AGO4) loaded witha 24 nucleotide siRNA binds to Pol V transcripts and, in an unknownfashion, acts to direct DRM2 to DNA for methylation (Law et al., 2010;Pikaard et al., 2008; Wierzbicki et al., 2009).

It is clear that there are a multitude of proteins involved in theepigenetic regulation of plant genomes. Applicants have previously shownthat a protein called SHH1 acts in the RdDM pathway to enable siRNAproduction from RdDM targets and that SHH1 is required for RNApolymerase IV (Pol IV) occupancy at these target loci. Applicants havealso previously shown that Pol V association with chromatin is dependenton two proteins called SUVH2 and SUVH9. These results have alsohighlighted that the RdDM pathway is a self-reinforcing loop mechanism,meaning that targeting of various components in different parts of thepathway to DNA are likely to initiate the entire pathway and causeRNA-directed DNA methylation.

The present disclosure is based, at least in part, on Applicant'sdiscovery that various epigenetic regulators may be recombinantly fusedto a zinc finger DNA-binding domain that targets a specific nucleic acidsequence, and that the targeted nucleic acid is then silenced in plantsharboring the genetically modified epigenetic regulator. Epigeneticregulators where this approach has been successful, as described herein,include e.g. SHH1, SHH2, AGO4, HDA6, NRPD1, NRPE1, JMJ14, RDR2, andNRPD2A/NRPE2. Advantageously, and without wishing to be bound by theory,such recombinant proteins can be used to recruit Pol IV and/or Pol V totarget loci to induce RNA-directed DNA methylation at the target loci,and thus to silence the target loci.

Of particular note, Applicants have shown that various components of RNAPol IV (e.g. NRPD1) and RNA Pol V (e.g. NRPE2) can be directly targetedto a specific locus using the methods of the present disclosure, asopposed to being recruited to the target locus via other epigeneticregulators involved in the RNA-directed DNA methylation pathwayaccording to the methods of the present disclosure. Various othercomponents of RNA Pol IV and/or RNA Pol V may be used according to themethods of the present disclosure to target RNA Pol IV and/or RNA Pol Vto a target locus and silence the locus.

Other exemplary proteins useful in the methods of the present disclosurefor targeting Pol IV, Pol V, DNA methylation, and/or gene silencing tospecific loci include e.g. any one of a modified NRPB3/NRPD3/NRPE3A,NRPE3B, NRPB11/NRPD11/NRPE11, NRPB10/NRPD10/NRPE10,NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A, NRPB6B/NRPD6B/NRPE6B,NRPB8A/NRPE8A, NRPB8B/NRPD8B/NRPE8B, NRPE5, NRPD4/NRPE4, NRPE7, NRPD7,NRPB5/NRPD5, NRPB9A/NRPD9A/NRPE9A, NRPB9B/NRPD9B/NRPE9B, ATRX, MOM1,MORC1, SssI, DRM2-MTase, DNMT3A, DNMT3L, MBD9, SUVH2, SUVH9, DMS3,MORC6, SUVR2, DRD1, RDM1, DRM3, DRM2, FRG, and homologs and orthologsthereof. These proteins may be engineered to specifically bind differentDNA sequences by introducing a heterologous DNA-binding domain into theprotein or a fragment of the protein such as, for example, aheterologous zinc finger domain or TAL effector targeting domain.

Accordingly, the present disclosure provides methods for silencingspecific loci in plants using one or more of an SHH1 protein, an SHH2protein, an AGO4 protein, an HDA6 protein, an NRPD1 protein, an NRPE1protein, a JMJ14 protein, an RDR2 protein, an NRPD2A/NRPE2 protein, anNRPB3/NRPD3/NRPE3A protein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11protein, an NRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12protein, an NRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6Bprotein, an NRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, anNRPE5 protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7protein, an NRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, an RDM1protein, a DRM3 protein, a DRM2 protein, and/or an FRG protein that havebeen engineered to specifically bind different DNA sequences via theintroduction of a heterologous DNA-binding domain into the protein. Eachone of the aforementioned modified proteins may be expressed in a hostcell individually or in various combinations to act to silence a targetlocus. For example, a modified SHH1 protein having a heterologousDNA-binding domain may be expressed in a host cell to target Pol IV to atarget locus in conjunction with one or more modified epigeneticregulators having a heterologous DNA-binding domain to target Pol V tothat same target locus to trigger RNA-directed DNA methylation andepigenetic silencing of that target locus.

The present disclosure also provides modified epigenetic regulators suchas, for example, a modified SHH1, SHH2, AGO4, HDA6, NRPD1, NRPE1, JMJ14,RDR2, NRPD2A/NRPE2, NRPB3/NRPD3/NRPE3A, NRPE3B, NRPB11/NRPD11/NRPE11,NRPB10/NRPD10/NRPE10, NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A,NRPB6B/NRPD6B/NRPE6B, NRPB8A/NRPE8A, NRPB8B/NRPD8B/NRPE8B, NRPE5,NRPD4/NRPE4, NRPE7, NRPD7, NRPB5/NRPD5, NRPB9A/NRPD9A/NRPE9A,NRPB9B/NRPD9B/NRPE9B, ATRX, MOM1, MORC1, SssI, DRM2-MTase, DNMT3A,DNMT3L, MBD9, SUVH2, SUVH9, DMS3, MORC6, SUVR2, DRD1, RDM1, DRM3, DRM2,and/or FRG protein that can be targeted to a specific locus of interestusing a CRISPR-CAS9 targeting system. CRISPR-CAS9 systems involve theuse of a CRISPR RNA (crRNA), a trans-activating CRISPR RNA (tracrRNA),and a CAS9 protein. The crRNA and tracrRNA aid in directing the CAS9protein to a target nucleic acid sequence, and these RNA molecules canbe specifically engineered to target specific nucleic acid sequences. Inparticular, certain aspects of the present disclosure involve the use ofa single guide RNA (gRNA) that reconstitutes the function of the .crRNAand the tracrRNA. Further, certain aspects of the present disclosureinvolve a CAS9 protein that does not exhibit DNA cleavage activity(dCAS9). As disclosed herein, gRNA molecules may be used to direct thedCAS9 protein to a target nucleic acid sequence. By recombinantly fusingan epigenetic regulator of the present disclosure to a dCAS9 protein,use of the CRISPR targeting system allows for delivering an epigeneticregulator directly to a target nucleic acid. Once at the target nucleicacid, the epigenetic regulator can act to induce RNA-directed DNAmethylation and epigenetic silencing of the target nucleic acid.

Accordingly, the present disclosure provides methods forCRISPR-targeting of an epigenetic regulator to a specific locus and forsilencing that target locus in host cells using one or more proteins ofthe present disclosure such as, for example, an SHH1 protein, an SHH2protein, an AGO4 protein, an HDA6 protein, an NRPD1 protein, an NRPE1protein, a JMJ14 protein, an RDR2 protein, an NRPD2A/NRPE2 protein, anNRPB3/NRPD3/NRPE3A protein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11protein, an NRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12protein, an NRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6Bprotein, an NRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, anNRPE5 protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7protein, an NRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, an RDM1protein, a DRM3 protein, a DRM2 protein, and/or an FRG protein that isrecombinantly fused to a CAS9 protein, such as a nuclease-deficient CAS9protein. The methods of the present disclosure also involve the use of acrRNA and tracrRNA to interact with the target nucleic acid to besilenced. The crRNA and tracrRNA directs the recombinant protein of thepresent disclosure fused to a CAS9 protein to the target nucleic acid,thereby facilitating the epigenetic silencing of the target nucleicacid.

Each one of the aforementioned modified proteins may be expressed in ahost cell individually or in various combinations to act to silence atarget locus. For example, a modified SHH1 protein recombinantly fusedto a CAS9 protein may be expressed in a host cell to target Pol IVand/or Pol V to a target locus in conjunction with one or more of themodified epigenetic regulators of the present disclosure to triggerRNA-directed DNA methylation and epigenetic silencing of that targetlocus.

The methods of the present disclosure for silencing target loci in hostcells may also involve the introduction of small interfering RNAs(siRNAs) at a target locus in conjunction with Pol V targeting by one ormore proteins of the present disclosure. Methods of generating siRNAsare well-known in the art. These methods include, for example,expression of hairpin RNAs that are naturally processed into smallinterfering RNAs in cells. Hairpin constructs that make smallinterfering RNAs are known in the art (EMBO Reports, 2006 November;7(11):1168-75). Additional methods for generating siRNAs include, forexample, the direct introduction of small interfering RNAs into a cellfrom exogenous sources. Methods describing bombardment of siRNAs intoplants are known in the art (Science 328, 912 (2010)). RNA molecules mayalso be sprayed (exogenous application) onto a plant so that small RNAscan then be generated in a plant cell (See U.S. Patent Application2014/0018241). Accordingly, the methods of the present disclosure forsilencing target loci in host cells may also involve the introduction ofsmall interfering RNAs (siRNAs) at a target locus in conjunction withPol V targeting by one or more modified epigenetic regulators of thepresent disclosure.

Accordingly, certain aspects of the present disclosure relate totargeting an epigenetic regulator to a target nucleic acid using one ormore SHH1-like proteins, SHH2-like proteins, AGO4-like proteins,HDA6-like proteins, NRPD1-like proteins, NRPE1-like proteins, JMJ14-likeproteins, RDR2-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1 likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins, or a fragment of the full-length coding sequence thereof, aswell as containing a heterologous coding sequence that encodes a proteininvolved in the targeting and/or recruitment of the respectiveepigenetic regulator to a target nucleic acid via the CRISPR-CAS9system. Thus, in some embodiments, SHH1-like proteins, SHH2-likeproteins, AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins,NRPE1-like proteins, JMJ14-like proteins, RDR2-like proteins,NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-like proteins,NRPE3B-like proteins, NRPB11/NRPD11/NRPE11-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB12/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1 like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins are fusion proteins that have been engineeredto specifically bind different DNA sequences via the introduction of aheterologous DNA-binding domain into the epigenetic regulator protein.Further, in some embodiments, SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB2/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1 likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins are fusion proteins that are able to target and silence aspecific nucleic acid with the use of an engineered CRISPR-CAS9targeting system. The respective SHH1 protein, SHH2 protein, AGO4protein, HDA6 protein, NRPD1 protein, NRPE1 protein, JMJ14 protein, RDR2protein, NRPD2A/NRPE2 protein, NRPB3/NRPD3/NRPE3A protein, NRPE3Bprotein, NRPB11/NRPD11/NRPE11 protein, NRPB10/NRPD10/NRPE10 protein,NRPB12/NRPD12/NRPE12 protein, NRPB6A/NRPD6A/NRPE6A protein,NRPB6B/NRPD6B/NRPE6B protein, NRPB8A/NRPE8A protein,NRPB8B/NRPD8B/NRPE8B protein, NRPE5 protein, NRPD4/NRPE4 protein, NRPE7protein, NRPD7 protein, NRPB5/NRPD5 protein, NRPB9A/NRPD9A/NRPE9Aprotein, NRPB9B/NRPD9B/NRPE9B protein, ATRX protein, MOM1 protein, MORC1protein, SssI protein, DRM2-MTase protein, DNMT3A protein, DNMT3Lprotein, MBD9 protein, SUVH2 protein, SUVH9 protein, DMS3 protein, MORC6protein, SUVR2 protein, DRD1 protein, RDM1 protein, DRM3 protein, DRM2protein, and/or FRG protein portion of the corresponding epigeneticregulator-like protein may be present in various N-terminal orC-terminal orientations relative to the heterologous coding sequence.

Epigenetic regulators of the present disclosure such as, for example,any one of SHH1-like proteins, SHH2-like proteins, AGO4-like proteins,HDA6-like proteins, NRPD1-like proteins, NRPE1-like proteins, JMJ14-likeproteins, RDR2-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1 likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins may be combined and expressed in a host cell in variouscombinations.

In some embodiments, a JMJ14-like protein and an HDA6-like protein asdescribed herein may be expressed in a host cell. In some embodiments,an SHH1-like protein, a DMS3-like protein, an HDA6-like protein, and aJMJ14-like protein may all be expressed in a host cell.

DNA-Binding Domains

Certain aspects of the present disclosure relate to epigeneticregulator-like proteins such as, for example, SHH1-like proteins,SHH2-like proteins, AGO4-like proteins, HDA6-like proteins, NRPD1-likeproteins, NRPE1-like proteins, JMJ14-like proteins, RDR2-like proteins,NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-like proteins,NRPE3B-like proteins, NRPB11/NRPD11/NRPE11-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB12/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1 like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins of the present disclosure, that haveDNA-binding activity. In some embodiments, this DNA-binding activity isachieved through a heterologous DNA-binding domain (e.g. binds with asequence affinity other than that of a DNA-binding domain that may bepresent in the endogenous protein). In some embodiments, recombinantproteins of the present disclosure contain a DNA-binding domain.Recombinant proteins of the present disclosure may contain one DNAbinding domain or they may contain more than one DNA-binding domain.Heterologous DNA-binding domains may be recombinantly fused to anepigenetic regulator of the present disclosure such that the epigeneticregulator is then targeted to a specific nucleic acid sequence and caninduce silencing of the specific nucleic acid sequence.

In some embodiments, the DNA-binding domain is a zinc finger domain. Azinc finger domain generally refers to a DNA-binding protein domain thatcontains zinc fingers, which are small protein structural motifs thatcan coordinate one or more zinc ions to help stabilize their proteinfolding. Zinc fingers were first identified as DNA-binding motifs(Miller et al., 1985), and numerous other variations of them have beencharacterized. Recent progress has been made that allows the engineeringof DNA-binding proteins that specifically recognize any desired DNAsequence. For example, it was shown that a three-finger zinc fingerprotein could be constructed to block the expression of a human oncogenethat was transformed into a mouse cell line (Choo and Klug, 1994).

Zinc fingers can generally be classified into several differentstructural families and typically function as interaction modules thatbind DNA, RNA, proteins, or small molecules. Suitable zinc fingerdomains of the present disclosure may contain two, three, four, five,six, seven, eight, or nine zinc fingers. Examples of suitable zincfinger domains may include, for example, Cys2His2 (C2H2) zinc fingerdomains, C-x8-C-x5-C-x3-H (CCCH) zinc finger domains, multi-cysteinezinc finger domains, and zinc binuclear cluster domains.

In some embodiments, the DNA-binding domain binds a specific nucleicacid sequence. For example, the DNA-binding domain may bind a sequencethat is at least 5 nucleotides, at least 6 nucleotides, at least 7nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, atleast 20 nucleotides, at least 25 nucleotides, at least 30 nucleotides,at least 35 nucleotides, at least 40 nucleotides, at least 45nucleotides, at least 50 nucleotides, or a high number of nucleotides inlength.

In some embodiments, a recombinant protein of the present disclosurefurther contains two N-terminal CCCH zinc finger domains.

In some embodiments, the zinc finger domain is an engineered zinc fingerarray, such as a C2H2 zinc finger array. Engineered arrays of C2H2 zincfingers can be used to create DNA-binding proteins capable of targetingdesired genomic DNA sequences. Methods of engineering zinc finger arraysare well known in the art, and include, for example, combining smallerzinc fingers of known specificity.

In some embodiments, recombinant proteins of the present disclosure maycontain a DNA-binding domain other than a zinc finger domain. Examplesof such DNA-binding domains may include, for example, TAL (transcriptionactivator-like) effector targeting domains, helix-turn-helix familyDNA-binding domains, basic domains, ribbon-helix-helix domains, TBP(TATA-box binding protein) domains, barrel dimer domains, RHB domains(real homology domain), BAH (bromo-adjacent homology) domains, SANTdomains, Chromodomains, Tudor domains, Bromodomains, PHD domains (planthomeo domain), WD40 domains, and MBD domains (methyl-CpG-bindingdomain).

In some embodiments, the DNA-binding domain is a TAL effector targetingdomain. TAL effectors generally refer to secreted bacterial proteins,such as those secreted by Xanthomonas or Ralstonia bacteria wheninfecting various plant species. Generally, TAL effectors are capable ofbinding promoter sequences in the host plant, and activate theexpression of plant genes that aid in bacterial infection. TAL effectorsrecognize plant DNA sequences through a central repeat targeting domainthat contains a variable number of approximately 34 amino acid repeats.Moreover, TAL effector targeting domains can be engineered to targetspecific DNA sequences. Methods of modifying TAL effector targetingdomains are well known in the art, and described in Bogdanove andVoytas, Science. 2011 Sep. 30; 333(6051):1843-6.

Other DNA-binding domains for use in the methods and compositions of thepresent disclosure will be readily apparent to one of skill in the art,in view of the present disclosure.

CRISPR-CAS9

Certain methods of the present disclosure relate to using a CRISPR-CAS9targeting system to target an epigenetic regulator to a target nucleicacid and induce silencing of the target nucleic acid.

CRISPR systems naturally use small base-pairing guide RNAs to target andcleave foreign DNA elements in a sequence-specific manner (Wiedenheft etal., 2012). There are diverse CRISPR systems in different organisms thatmay be used to target proteins of the present disclosure to a targetnucleic acid. One of the simplest systems is the type II CRISPR systemfrom Streptococcus pyogenes. Only a single gene encoding the CAS9protein and two RNAs, a mature CRISPR RNA (crRNA) and a partiallycomplementary trans-acting RNA (tracrRNA), are necessary and sufficientfor RNA-guided silencing of foreign DNAs (Jinek et al., 2012).Maturation of crRNA requires tracrRNA and RNase III (Deltcheva et al.,2011). However, this requirement can be bypassed by using an engineeredsmall guide RNA (gRNA) containing a designed hairpin that mimics thetracrRNA-crRNA complex (Jinek et al., 2012). Base pairing between thegRNA and target DNA normally causes double-strand breaks (DSBs) due tothe endonuclease activity of CAS9.

It is known that the endonuclease domains of the CAS9 protein can bemutated to create a programmable RNA-dependent DNA-binding protein(dCAS9) (Qi et al., 2013). The fact that duplex gRNA-dCAS9 binds targetsequences without endonuclease activity has been used to tetherregulatory proteins, such as transcriptional activators or repressors,to promoter regions in order to modify gene expression (Gilbert et al.,2013), and CAS9 transcriptional activators have been used for targetspecificity screening and paired nickases for cooperative genomeengineering (Mali et al., 2013, Nature Biotechnology 31:833-838). Thus,dCAS9 may be used as a modular RNA-guided platform to recruit differentproteins to DNA in a highly specific manner. One of skill in the artwould recognize other RNA-guided DNA binding protein/RNA complexes thatcan be used equivalently to CRISPR-CAS9.

The CRISPR-CAS9 system may be used to target an epigenetic regulator ofthe present disclosure such as, for example, one or more of an SHH1protein, an SHH2 protein, an AGO4 protein, an HDA6 protein, an NRPD1protein, an NRPE1 protein, a JMJ14 protein, an RDR2 protein, anNRPD2A/NRPE2 protein, an NRPB3/NRPD3/NRPE3A protein, an NRPE3B protein,an NRPB11/NRPD11/NRPE11 protein, an NRPB10/NRPD10/NRPE10 protein, anNRPB12/NRPD12/NRPE12 protein, an NRPB6A/NRPD6A/NRPE6A protein, anNRPB6B/NRPD6B/NRPE6B protein, an NRPB8A/NRPE8A protein, anNRPB8B/NRPD8B/NRPE8B protein, an NRPE5 protein, an NRPD4/NRPE4 protein,an NRPE7 protein, an NRPD7 protein, an NRPB5/NRPD5 protein, anNRPB9A/NRPD9A/NRPE9A protein, an NRPB9B/NRPD9B/NRPE9B protein, an ATRXprotein, a MOM1 protein, a MORC1 protein, an SssI protein, a DRM2-MTaseprotein, a DNMT3A protein, a DNMT3L protein, a MBD9 protein, a SUVH2protein, a SUVH9 protein, a DMS3 protein, a MORC6 protein, a SUVR2protein, a DRD1 protein, an RDM1 protein, a DRM3 protein, a DRM2protein, and/or an FRG protein to a specific nucleic acid.

Targeting using CRISPR-CAS9 may be beneficial over other genometargeting techniques in certain instances. For example, one need onlychange the guide RNAs in order to target fusion proteins to a newgenomic location, or even multiple locations simultaneously. Further,CAS9-mediated targeting has been shown to be insensitive to themethylation state of the target nucleic acid (Nature Biotechnology 31,827-832 (2013)). In addition, guide RNAs can be extended to includesites for binding to proteins, such as the MS2 protein, which can befused to proteins of interest.

CAS9 Proteins

A variety of CAS9 proteins may be used in the methods of the presentdisclosure. There are several CAS9 genes present in different bacteriaspecies (Esvelt, K et al, 2013, Nature Methods). One of the mostcharacterized CAS9 proteins is the CAS9 protein from S. pyogenes that,in order to be active, needs to bind a gRNA with a specific sequence andthe presence of a PAM motif (NGG, where N is any nucleotide) at the 3′end of the target locus. However, other CAS9 proteins from differentbacterial species show differences in 1) the sequence of the gRNA theycan bind and 2) the sequence of the PAM motif. Therefore, it is possiblethat other CAS9 proteins such as, for example, those from Streptococcusthermophilus or N. meningitidis may also be utilized herein. Indeed,these two CAS9 proteins have a smaller size (around 1100 amino acids) ascompared to S. pyogenes CAS9 (1400 amino acids), which may confer someadvantages during cloning or protein expression.

CAS9 proteins from a variety of bacteria have been used successfully inengineered CRISPR-CAS9 systems. There are also versions of CAS9 proteinsavailable in which the codon usage has been more highly optimized forexpression in eukaryotic systems, such as human codon optimized CAS9(Cell, 152:1173-1183) and plant optimized CAS9 (Nature Biotechnology,31:688-691).

CAS9 proteins may also be modified for various purposes. For example,CAS9 proteins may be engineered to contain a nuclear-localizationsequence (NLS). CAS9 proteins may be engineered to contain an NLS at theN-terminus of the protein, at the C-terminus of the protein, or at boththe N- and C-terminus of the protein. Engineering a CAS9 protein tocontain an NLS may assist with directing the protein to the nucleus of ahost cell. CAS9 proteins may be engineered such that they are unable tocleave nucleic acids (e.g. nuclease-deficient dCAS9 polypeptides). Oneof skill in the art would be able to readily identify a suitable CAS9protein for use in the methods and compositions of the presentdisclosure.

Exemplary CAS9 proteins that may be used in the methods and compositionsof the present disclosure may include, for example, a CAS9 proteinhaving the amino acid sequence of any one of SEQ ID NO: 401, SEQ ID NO:402, and/or SEQ ID NO: 403, homologs thereof, and fragments thereof.

In some embodiments, a CAS9 polypeptide or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofSEQ ID NO: 401, SEQ ID NO: 402, or SEQ ID NO: 403. In some embodiments,the CAS9 polypeptide does not have nuclease activity and is unable tocleave a nucleic acid molecule (e.g. dCAS9 polypeptide).

CRISPR RNAs

The CRISPR RNA (crRNA) of the present disclosure may take a variety offorms. As described above, the sequence of the crRNA is involved inconferring specificity to targeting a specific nucleic acid.

Many different crRNA molecules can be designed to target many differentsequences.

With respect to targeting, target nucleic acids generally require thePAM sequence, NGG, at the end of the 20 base pair target sequence.crRNAs of the present disclosure may be expressed as a single crRNAmolecule, or they may be expressed in the form of a crRNA/tracrRNAhybrid molecule where the crRNA and the tracrRNA have been fusedtogether, forming a guide RNA (gRNA). crRNA molecules and/or guide RNAmolecules may be extended to include sites for the binding of RNAbinding proteins.

Multiple crRNAs and/or guide RNAs can be encoded into a single CRISPRarray to enable simultaneous targeting to several sites (Science 2013:Vol. pp. 819-823). For example, the tracrRNA may be expressedseparately, and two adjacent target sequences may be encoded in apre-crRNA array interspaced with repeats.

A variety of promoters may be used to drive expression of the crRNAand/or the guide RNA. crRNAs and/or guide RNAs may be expressed using aPol III promoter such as, for example, the U6 promoter or the H1promoter (eLife 2013 2:e00471). For example, an approach in plants hasbeen described using three different Pol III promoters from threedifferent Arabidopsis U6 genes, and their corresponding gene terminators(BMC Plant Biology 2014 14:327). One skilled in the art would readilyunderstand that many additional Pol III promoters could be utilized tosimultaneously express many crRNAs and/or guide RNAs to many differentlocations in the genome simultaneously. The use of different Pol IIIpromoters for each crRNA and/or gRNA expression cassette may bedesirable to reduce the chances of natural gene silencing that can occurwhen multiple copies of identical sequences are expressed in plants. Inaddition, crRNAs and/or guide RNAs can be modified to improve theefficiency of their function in guiding CAS9 to a target nucleic acid.For example, it has been shown that adding either 8 or 20 additionalnucleotides to the gRNA in order to extend the hairpin by 4 or 10 basepairs resulted in more efficient CAS9 activity (eLife 2013 2:e00471).

Alternatively, a tRNA-gRNA expression cassette (Xie, X et al, 2015, ProcNatl Acad Sci USA. 2015 Mar. 17; 112(11):3570-5) may be used to delivermultiple gRNAs simultaneously with high expression levels.

Trans-Activating CRISPR RNAs

The trans-activating CRISPR RNA (tracrRNA) of the present disclosure maytake a variety of forms, as will be readily understood by one of skillin the art. As described above, tracrRNAs are involved in the maturationof a crRNA. tracrRNAs of the present disclosure may be expressed as asingle tracrRNA molecule, or they may be expressed in the form of acrRNA/tracrRNA hybrid molecule where the crRNA and the tracrRNA havebeen fused together, forming a guide RNA (gRNA). tracrRNA moleculesand/or guide RNA molecules may be extended to include sites for thebinding of RNA binding proteins.

As CRISPR systems naturally exist in a variety of bacteria, theframework of the crRNA and tracrRNA in these bacteria may be adapted foruse in the methods and compositions described herein. crRNAs, tracrRNAs,and/or guide RNAs of the present disclosure may be constructed based onthe framework of one or more of these molecules in, for example, S.pyogenes, Streptococcus thermophilus, and/or N. meningitidis. Forexample, a guide RNA of the present disclosure may be constructed basedon the framework of the crRNA and tracrRNA from S. pyogenes (SEQ ID NO:404), Streptococcus thermophilus (SEQ ID NO: 405), and/or N.meningitidis (SEQ ID NO: 406). In these exemplary frameworks, the 5′ endof the sequence contains 20 generic nucleotides (N) that correspond tothe crRNA targeting sequence. This sequence will vary depending on thesequence of the particular nucleic acid being targeted.

Linkers

Various linkers may be used in the construction of recombinant proteinsas described herein. In general, linkers are short peptides thatseparate the different domains in a multi-domain protein. They may playan important role in fusion proteins, affecting the crosstalk betweenthe different domains, the yield of protein production, and thestability and/or the activity of the fusion proteins. Linkers aregenerally classified into 2 major categories: flexible or rigid.Flexible linkers are typically used when the fused domains require acertain degree of movement or interaction, and these linkers are usuallycomposed of small amino acids such as, for example, glycine (G), serine(S) or proline (P).

The certain degree of movement between domains allowed by flexiblelinkers is an advantage in some fusion proteins. However, it has beenreported that flexible linkers can sometimes reduce protein activity dueto an inefficient separation of the two domains. In this case, rigidlinkers may be used since they enforce a fixed distance between domainsand promote their independent functions. A thorough description ofseveral linkers has been provided in Chen X et al., 2013, Advanced DrugDelivery Reviews 65 (2013) 1357-1369).

Various linkers may be used in, for example, the construction ofrecombinant epigenetic regulators that are fused to a CAS9 protein asdescribed herein. Linkers may be used in the epigenetic regulator-CAS9fusion proteins described herein to separate the coding sequences of anepigenetic regulator of the present disclosure and a CAS9 protein. Forexample, a variety of wiggly/flexible linkers, stiff/rigid linkers,short linkers, and long linkers may be used as described herein. Variouslinkers as described herein may be used in the construction of one ormore SHH1-like proteins, SHH2-like proteins, AGO4-like proteins,HDA6-like proteins, NRPD1-like proteins, NRPE1-like proteins, JMJ14-likeproteins, RDR2-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1 likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins as described herein. Linkers may also be used in otherrecombinant polypeptides as described herein (e.g. recombinantpolypeptides in a SunTag system).

A variety of shorter or longer linker regions are known in the art, forexample corresponding to a series of glycine residues, a series ofadjacent glycine-serine dipeptides, a series of adjacentglycine-glycine-serine tripeptides, or known linkers from otherproteins. A flexible linker may include, for example, the amino acidsequence: SSGPPPGTG and variants thereof. A rigid linker may include,for example, the amino acid sequence: AEAAAKEAAAKA (SEQ ID NO: 863) andvariants thereof. The XTEN linker, SGSETPGTSESATPES (SEQ ID NO: 864),and variants thereof, described in Guilinget et al, 2014 (NatureBiotechnology 32, 577-582), may also be used. This particular linker waspreviously shown to produce the best results among other linkers in aprotein fusion between dCAS9 and the nuclease FokI.

Variations of CRISPR-CAS9 Targeting

Certain aspects of the present disclosure relate to recombinantly fusinga polypeptide of the present disclosure such as, for example, an SHH1protein, an SHH2 protein, an AGO4 protein, an HDA6 protein, an NRPD1protein, an NRPE1 protein, a JMJ14 protein, an RDR2 protein, anNRPD2A/NRPE2 protein, an NRPB3/NRPD3/NRPE3A protein, an NRPE3B protein,an NRPB11/NRPD11/NRPE11 protein, an NRPB10/NRPD10/NRPE10 protein, anNRPB12/NRPD12/NRPE12 protein, an NRPB6A/NRPD6A/NRPE6A protein, anNRPB6B/NRPD6B/NRPE6B protein, an NRPB8A/NRPE8A protein, anNRPB8B/NRPD8B/NRPE8B protein, an NRPE5 protein, an NRPD4/NRPE4 protein,an NRPE7 protein, an NRPD7 protein, an NRPB5/NRPD5 protein, anNRPB9A/NRPD9A/NRPE9A protein, an NRPB9B/NRPD9B/NRPE9B protein, an ATRXprotein, a MOM1 protein, a MORC1 protein, an SssI protein, a DRM2-MTaseprotein, a DNMT3A protein, a DNMT3L protein, a MBD9 protein, a SUVH2protein, a SUVH9 protein, a DMS3 protein, a MORC6 protein, a SUVR2protein, a DRD1 protein, a RDM1 protein, a DRM3 protein, a DRM2 protein,and/or a FRG protein to a CAS9 protein. However, CRISPR-CAS9 targetingschemes as described herein to target a specific nucleic acid may alsoinvolve schemes where a polypeptide of the present disclosure istargeted to a specific nucleic acid without being recombinantly fused toa CAS9 protein.

The use of recombinant proteins containing an epigenetic regulatorrecombinantly fused to an RNA-binding protein may be used in targetingof the epigenetic regulator to a specific nucleic acid via CRISPR-CAS9targeting. In some embodiments, an SHH1 protein, an SHH2 protein, anAGO4 protein, an HDA6 protein, an NRPD1 protein, an NRPE1 protein, aJMJ14 protein, an RDR2 protein, an NRPD2A/NRPE2 protein, anNRPB3/NRPD3/NRPE3A protein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11protein, an NRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12protein, an NRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6Bprotein, an NRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, anNRPE5 protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7protein, an NRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, a RDM1protein, a DRM3 protein, a DRM2 protein, and/or a FRG protein isrecombinantly fused to an MS2 coat protein such that these fusionproteins may be directed to a target nucleic acid with the assistance ofa CAS9 protein. Various MS2 coat proteins may be used, such as SEQ IDNO: 407 and homologs thereof. This targeting scheme is further describedherein and will be readily understood by one of skill in the art in viewof the present disclosure.

In addition to fusing an epigenetic regulator to an MS2 coat protein,other RNA-binding proteins may also be used in this targeting scheme.For example, the proteins PP7 and COM (Zalatan et al., Cell 160,339-350), may also be recombinantly fused to an SHH1 protein, an SHH2protein, an AGO4 protein, an HDA6 protein, an NRPD1 protein, an NRPE1protein, a JMJ14 protein, an NRPD2A/NRPE2 protein, an NRPB3/NRPD3/NRPE3Aprotein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11 protein, anNRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12 protein, anNRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6B protein, anNRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, an NRPE5protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7 protein, anNRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, a RDM1protein, a DRM3 protein, a DRM2 protein, and/or a FRG protein such thatthese fusion proteins may be directed to a target nucleic acid with theassistance of a CAS9 protein.

The use of recombinant proteins containing an epigenetic regulatorrecombinantly fused to an antibody or fragment thereof may be used intargeting of the epigenetic regulator to a specific nucleic acid viaCRISPR-CAS9 targeting. In some embodiments, an SHH1 protein, an SHH2protein, an AGO4 protein, an HDA6 protein, an NRPD1 protein, an NRPE1protein, a JMJ14 protein, an RDR2 protein, an NRPD2A/NRPE2 protein, anNRPB3/NRPD3/NRPE3A protein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11protein, an NRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12protein, an NRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6Bprotein, an NRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, anNRPE5 protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7protein, an NRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, an RDM1protein, a DRM3 protein, a DRM2 protein, and/or an FRG protein isrecombinantly fused to an scFV antibody such that these fusion proteinsmay be directed to a target nucleic acid with the assistance of a CAS9protein. Various scFV antibodies may be used, such as SEQ ID NO: 408 andhomologs thereof. This targeting scheme is further described herein andwill be readily understood by one of skill in the art in view of thepresent disclosure.

Similar systems using antibody mimetic proteins or proteins which canbind other proteins may also be used in the methods described herein.For example, designed ankyrin repeat proteins (DARPins), which are smalland highly stable proteins that can bind their epitopes with strongaffinity (Binz et al., 2004, Nat. Biotechnol. 22, 575-582), may berecombinantly fused to an SHH1 protein, an SHH2 protein, an AGO4protein, an HDA6 protein, an NRPD1 protein, an NRPE1 protein, a JMJ14protein, an RDR2 protein, an NRPD2A/NRPE2 protein, an NRPB3/NRPD3/NRPE3Aprotein, an NRPE3B protein, an NRPB11/NRPD11/NRPE11 protein, anNRPB10/NRPD10/NRPE10 protein, an NRPB12/NRPD12/NRPE12 protein, anNRPB6A/NRPD6A/NRPE6A protein, an NRPB6B/NRPD6B/NRPE6B protein, anNRPB8A/NRPE8A protein, an NRPB8B/NRPD8B/NRPE8B protein, an NRPE5protein, an NRPD4/NRPE4 protein, an NRPE7 protein, an NRPD7 protein, anNRPB5/NRPD5 protein, an NRPB9A/NRPD9A/NRPE9A protein, anNRPB9B/NRPD9B/NRPE9B protein, an ATRX protein, a MOM1 protein, a MORC1protein, an SssI protein, a DRM2-MTase protein, a DNMT3A protein, aDNMT3L protein, a MBD9 protein, a SUVH2 protein, a SUVH9 protein, a DMS3protein, a MORC6 protein, a SUVR2 protein, a DRD1 protein, an RDM1protein, a DRM3 protein, a DRM2 protein, and/or an FRG protein such thatthese fusion proteins may be directed to a target nucleic acid with theassistance of a CAS9 protein.

SunTag Systems

Certain aspects of the present disclosure relate to the use of SunTagsystems for targeting (using CRISPR-based targeting) an epigeneticregulator of the present disclosure to a target nucleic acid. Asynthetic system was previously developed for use in mammals forrecruiting multiple copies of a protein to a target polypeptide chain,and this system was called a SunTag system (Tanenbaum et al.,2014)(WO2016011070). This system was also adapted so that the multiplecopies of the protein using the SunTag system could be targeted to anucleic acid using the CRISPR-Cas9 system (Tanenbaum et al., 2014).However, this system was developed for use in mammals. Provided hereinare methods and compositions for SunTag systems adapted to targetepigenetic regulators to specific loci in plants.

Accordingly, the present disclosure provides methods and compositionsfor the recruitment of multiple copies of an epigenetic regulator (e.g.DRM2-MTase, DNMT3A, DNMT3L, DNMT3A-DNMT3L polypeptide fusions) to atarget nucleic acid in plants via CRISPR-based targeting in a mannerthat allows for methylation and/or silencing of the target nucleic acid.In certain aspects, this specific targeting involves the use of a systemthat includes (1) a nuclease-deficient CAS9 polypeptide that isrecombinantly fused to a multimerized epitope, (2) an epigeneticregulator polypeptide (e.g. DRM2-MTase, DNMT3A, DNMT3L, DNMT3A-DNMT3Lpolypeptide fusions) that is recombinantly fused to an affinitypolypeptide, and (3) a guide RNA (gRNA). In this aspect, the dCAS9portion of the dCAS9-multimerized epitope fusion protein is involvedwith targeting a target nucleic acid as directed by the guide RNA. Themultimerized epitope portion of the dCAS9-multimerized epitope fusionprotein is involved with binding to the affinity polypeptide (which isrecombinantly fused to an epigenetic regulator). The affinitypolypeptide portion of the epigenetic regulator-affinity polypeptidefusion protein is involved with binding to the multimerized epitope sothat the epigenetic regulator can be in association with dCAS9. Theepigenetic regulator portion of the epigenetic regulator-affinitypolypeptide fusion protein is involved with inducing methylation and/orsilencing of a target nucleic acid, once the complex has been targetedto a target nucleic acid via the guide RNA.

As described above, SunTag systems involve targeting based onCRISPR-CAS9 systems. CRISPR-CAS9 systems are described above. Thefeatures of CRISPR-CAS9 systems may be used in SunTag systems of thepresent disclosure as appropriate, as will be readily understood by oneof skill in the art.

Affinity Polypeptides

Certain aspects of the present disclosure relate to recombinantpolypeptides that contain an affinity polypeptide. Affinity polypeptidesof the present disclosure may bind to one or more epitopes (e.g. amultimerized epitope). In some embodiments, an affinity polypeptide ispresent in a recombinant polypeptide that contains an epigeneticregulator polypeptide (e.g. DRM2-MTase, DNMT3A, DNMT3L, DNMT3A-DNMT3Lpolypeptide fusions) and an affinity polypeptide.

A variety of affinity polypeptides are known in the art and may be usedherein. Generally, the affinity polypeptide should be stable in theconditions present in the intracellular environment of a plant cell.Additionally, the affinity polypeptide should specifically bind to itscorresponding epitope with minimal cross-reactivity.

The affinity polypeptide may be an antibody such as, for example, anscFv. The antibody may be optimized for stability in the plantintracellular environment. When a GCN4 epitope is used in the methodsdescribed herein, a suitable affinity polypeptide that is an antibodymay contain an anti-GCN4 scFv domain.

In embodiments where the affinity polypeptide is an scFv antibody, thepolypeptide may contain an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofSEQ ID NO: 793.

Other exemplary affinity polypeptides include, for example, proteinswith SH2 domains or the domain itself, 14-3-3 proteins, proteins withSH3 domains or the domain itself, the Alpha-Syntrophin PDZ proteininteraction domain, the PDZ signal sequence, or proteins from plantswhich can recognize AGO hook motifs (e.g. AGO4 from Arabidopsisthaliana).

Additional affinity polypeptides that may be used in the methods andcompositions described herein will be readily apparent to those of skillin the art.

Epitopes and Multimerized Epitopes

Certain aspects of the present disclosure relate to recombinantpolypeptides that contain an epitope or a multimerized epitope. Epitopesof the present disclosure may bind to an affinity polypeptide. In someembodiments, an epitope or multimerized epitope is present in arecombinant polypeptide that contains dCAS9 polypeptide.

Epitopes of the present disclosure may be used for recruiting affinitypolypeptides (and any polypeptides they may be recombinantly fused to)to a dCAS9 polypeptide. In embodiments where a dCAS9 polypeptide isfused to an epitope or a multimerized epitope, the dCAS9 polypeptide maybe fused to one copy of an epitope, multiple copies of an epitope, morethan one different epitope, or multiple copies of more than onedifferent epitope as further described herein.

A variety of epitopes and multimerized epitopes are known in the art andmay be used herein. In general, the epitope or multimerized epitope maybe any polypeptide sequence that is specifically recognized by anaffinity polypeptide of the present disclosure. Exemplary epitopes mayinclude a c-Myc affinity tag, an HA affinity tag, a His affinity tag, anS affinity tag, a methionine-His affinity tag, an RGD-His affinity tag,a FLAG octapeptide, a strep tag or strep tag II, a V5 tag, a VSV-Gepitope, and a GCN4 epitope.

Other exemplary amino acid sequences that may serve as epitopes andmultimerized epitopes include, for example, phosphorylated tyrosines inspecific sequence contexts recognized by SH2 domains, characteristicconsensus sequences containing phosphoserines recognized by 14-3-3proteins, proline rich peptide motifs recognized by SH3 domains, the PDZprotein interaction domain or the PDZ signal sequence, and the AGO hookmotif from plants.

Epitopes described herein may also be multimerized. Multimerizedepitopes may include at least 2, at least 3, at least 4, at least 5, atleast 6, at least 7, at least 8, at least 9, at least 10, at least 11,at least 12, at least 13, at least 14, at least 15, at least 16, atleast 17, at least 18, at least 19, at least 20, at least 21, at least22, at least 23, or at least 24 or more copies of an epitope.

Multimerized epitopes may be present as tandem copies of an epitope, oreach individual epitope may be separated from another epitope in themultimerized epitope by a linker or other amino acid sequence. Suitablelinker regions are known in the art and are described herein. The linkermay be configured to allow the binding of affinity polypeptides toadjacent epitopes without, or without substantial, steric hindrance.Linker sequences may also be configured to provide an unstructured orlinear region of the polypeptide to which they are recombinantly fused.The linker sequence may comprise e.g. one or more glycines and/orserines. The linker sequences may be e.g. at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, orat least 10 or more amino acids in length.

In some embodiments, the epitope is a GCN4 epitope (SEQ ID NO: 806). Insome embodiments, the multimerized epitope contains at least 2, at least3, at least 4, at least 5, at least 6, at least 7, at least 8, at least9, at least 10, at least 11, at least 12, at least 13, at least 14, atleast 15, at least 16, at least 17, at least 18, at least 19, at least20, at least 21, at least 22, at least 23, or at least 24 copies of aGCN4 epitope. In some embodiments, the multimerized epitope contains 10copies of a GCN4 epitope.

Additional epitopes and multimerized epitopes that may be used in themethods and compositions described herein will be readily apparent tothose of skill in the art.

Recombinant Proteins of the Present Disclosure

Certain methods of the present disclosure relate to reducing theexpression of a target nucleic acid in a plant by recombinantly fusingan epigenetic regulator polypeptide to a heterologous DNA-bindingdomain, where the DNA-binding domain is able to bind a specific nucleicacid sequence and thus the epigenetic regulator is targeted to thespecific nucleic acid sequence. Certain methods of the presentdisclosure relate to reducing the expression of a target nucleic acid ina plant by targeting an epigenetic regulator recombinantly fused to aCAS9 protein to the target nucleic acid. Certain methods of the presentdisclosure relate to reducing the expression of a target nucleic acid ina plant by targeting a recombinant epigenetic regulator to a targetnucleic acid with the assistance of a CAS9 protein. As used herein, a“polypeptide” is an amino acid sequence including a plurality ofconsecutive polymerized amino acid residues (e.g., at least about 15consecutive polymerized amino acid residues). “Polypeptide” refers to anamino acid sequence, oligopeptide, peptide, protein, or portionsthereof, and the terms “polypeptide” and “protein” are usedinterchangeably.

Accordingly, provided herein are recombinant proteins for use inreducing the expression of a target nucleic acid in a plant. In someembodiments, a recombinant protein of the present disclosure interactswith an RNA polymerase. This interaction may be direct or it may beindirect. Whether the interaction of a recombinant protein of thepresent disclosure with an RNA polymerase is direct or indirect, andwithout wishing to be bound by theory, it is though that the interactionfacilitates the recruitment of the RNA polymerase to a nucleic acid. Insome embodiments, one or more additional proteins may be furtherinvolved in facilitating the interaction of a recombinant protein of thepresent disclosure with an RNA polymerase and recruitment of the RNApolymerase to a nucleic acid. In some embodiments, a recombinant proteinof the present disclosure may interact, directly or indirectly, with RNAPol IV and this interaction facilitates the recruitment of RNA Pol IV toa nucleic acid. In some embodiments, a recombinant protein of thepresent disclosure may interact, directly or indirectly, with RNA Pol Vand this interaction facilitates the recruitment of RNA Pol V to anucleic acid. In some embodiments, the recombinant proteins of thepresent disclosure facilitate RNA-directed DNA methylation of a nucleicacid.

In some embodiments, recombinant proteins of the present disclosure suchas, for example, SHH1-like proteins, SHH2-like proteins, AGO4-likeproteins, HDA6-like proteins, NRPD1-like proteins, JMJ14-like proteins,RDR2-like proteins, NRPE1-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD1/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins are targeted to the same nucleic acid and cooperatively act tosilence the expression of the target nucleic acid. Recombinant proteinsof the present disclosure may be recombinantly expressed in a celleither alone or in combinations.

Polypeptides as described herein also include polypeptides havingvarious amino acid additions, deletions, or substitutions relative tothe native amino acid sequence of a polypeptide of the presentdisclosure. In some embodiments, polypeptides that are homologs of apolypeptide of the present disclosure contain non-conservative changesof certain amino acids relative to the native sequence of a polypeptideof the present disclosure. In some embodiments, polypeptides that arehomologs of a polypeptide of the present disclosure contain conservativechanges of certain amino acids relative to the native sequence of apolypeptide of the present disclosure, and thus may be referred to asconservatively modified variants. A conservatively modified variant mayinclude individual substitutions, deletions or additions to apolypeptide sequence which result in the substitution of an amino acidwith a chemically similar amino acid. Conservative substitution tablesproviding functionally similar amino acids are well-known in the art.Such conservatively modified variants are in addition to and do notexclude polymorphic variants, interspecies homologs, and alleles of thedisclosure. The following eight groups contain amino acids that areconservative substitutions for one another: 1) Alanine (A), Glycine (G);2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine(Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L),Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y),Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C),Methionine (M) (see, e.g., Creighton, Proteins (1984)). A modificationof an amino acid to produce a chemically similar amino acid may bereferred to as an analogous amino acid.

Recombinant polypeptides of the present disclosure that are composed ofindividual polypeptide domains may be described based on the individualpolypeptide domains of the overall recombinant polypeptide. A domain insuch a recombinant polypeptide refers to the particular stretches ofcontiguous amino acid sequences with a particular function or activity.For example, in a recombinant polypeptide that is a fusion of anepigenetic regulator polypeptide and an affinity polypeptide, thecontiguous amino acids that encode the epigenetic regulator polypeptidemay be described as the epigenetic regulator domain in the overallrecombinant polypeptide, and the contiguous amino acids that encode theaffinity polypeptide may be described as the affinity domain in theoverall recombinant polypeptide. Individual domains in an overallrecombinant protein may also be referred to as units of the recombinantprotein. Recombinant polypeptides that are composed of individualpolypeptide domains may also be referred to as fusion polypeptides.

Fusion polypeptides of the present disclosure may contain an individualpolypeptide domain that is in various N-terminal or C-terminalorientations relative to other individual polypeptide domains present inthe fusion polypeptide. Fusion of individual polypeptide domains infusion polypeptides may also be direct or indirect fusions. Directfusions of individual polypeptide domains refer to direct fusion of thecoding sequences of each respective individual polypeptide domain. Inembodiments where the fusion is indirect, a linker domain or othercontiguous amino acid sequence may separate the coding sequences of twoindividual polypeptide domains in a fusion polypeptide.

Nuclear Localization Signals (NLS)

Recombinant polypeptides of the present disclosure may contain one ormore nuclear localization signals (NLS). Nuclear localization signalsmay also be referred to as nuclear localization sequences, domains,peptides, or other terms readily apparent to those of skill in the art.Nuclear localization signals are a translocation sequence that, whenpresent in a polypeptide, direct that polypeptide to localize to thenucleus of a eukaryotic cell.

Various nuclear localization signals may be used in recombinantpolypeptides of the present disclosure. For example, one or moreSV40-type NLS or one or more REX NLS may be used in recombinantpolypeptides. Recombinant polypeptides may also contain two or moretandem copies of a nuclear localization signal. For example, recombinantpolypeptides may contain at least two, at least three, at least for, atleast five, at least six, at least seven, at least eight, at least nine,or at least ten copies, either tandem or not, of a nuclear localizationsignal.

Recombinant polypeptides of the present disclosure may contain one ormore nuclear localization signals that contain an amino acid sequencewith at least about 20%, at least about 25%, at least about 30%, atleast about 40%, at least about 50%, at least about 55%, at least about60%, at least about 65%, at least about 70%, at least about 75%, atleast about 80%, at least about 85%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at least about98%, at least about 99%, or at least about 100% amino acid identity tothe amino acid sequence of any one of SEQ ID NO: 779, SEQ ID NO: 797,and/or SEQ ID NO: 799.

SHH Proteins

Certain aspects of the present disclosure relate to SHH1-like proteins.In some embodiments, an SHH1-like protein refers to a recombinant SHH1protein or fragment thereof that contains a heterologous DNA-bindingdomain. In some embodiments, an SHH1-like protein refers to arecombinant SHH1 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an SHH1-like proteinrefers to a recombinant SHH1 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anSHH1-like protein refers to a recombinant SHH1 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. SHH1-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

SHH1 proteins of the present disclosure are SAWADEE HOMEODOMAIN HOMOLOG1 (SHH1) proteins. Full-length SHH1 proteins contain a homeodomain and achromatin-binding SAWADEE domain. The SAWADEE chromatin-binding domainadopts a unique tandem Tudor-like fold and functions as a dual lysinereader, probing for both unmethylated K4 and methylated K9 modificationson the histone 3 (H3) tail.

It was previously demonstrated that SHH1 is a chromatin-binding proteinthat functions in RdDM to enable Pol-IV recruitment and/or stability atthe most actively targeted genomic loci in order to promote siRNAbiogenesis (See WO/2014/134567, which is incorporated herein byreference in its entirety). Without wishing to be bound by theory, it isbelieved that the finding that SHH1 binds to repressive histonemodifications, together with the observation that SHH1 is required forPol IV chromatin association at a similar set of loci as downstream RdDMmutants, could explain the previously observed self-reinforcing loop inwhich downstream RdDM mutants are required for the production of fulllevels of siRNAs from a subset of genomic loci (Zilberman et al., 2004;Xie et al., 2004; Li et al., 2006; Pontes et al., 2006) as it has beenshown that downstream RdDM mutants can cause a reduction of both DNAmethylation and H3K9 methylation at RdDM loci (Zilberman et al., 2003).

In some embodiments, SHH1-like proteins of the present disclosure arechromatin-binding proteins. In some embodiments, an SHH1-like protein ofthe present disclosure includes a functional fragment of a full-lengthSHH1 protein where the fragment maintains the ability to recruit RNA PolIV to DNA. In some embodiments, an SHH1 protein fragment contains atleast 20 consecutive amino acids, at least 30 consecutive amino acids,at least 40 consecutive amino acids, at least 50 consecutive aminoacids, at least 60 consecutive amino acids, at least 70 consecutiveamino acids, at least 80 consecutive amino acids, at least 90consecutive amino acids, at least 100 consecutive amino acids, at least120 consecutive amino acids, at least 140 consecutive amino acids, atleast 160 consecutive amino acids, at least 180 consecutive amino acids,at least 200 consecutive amino acids, at least 220 consecutive aminoacids, at least 240 consecutive amino acids, or 241 or more consecutiveamino acids of a full-length SHH1 protein. In some embodiments, SHH1protein fragments may include sequences with one or more amino acidsremoved from the consecutive amino acid sequence of a full-length SHH1protein. In some embodiments, SHH1 protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length SHH1 protein. In some embodiments, SHH1 protein fragmentsmay include sequences with one or more amino acids added to an otherwiseconsecutive amino acid sequence of a full-length SHH1 protein.

Suitable SHH1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SHH1 proteins may include, for example, thoselisted in Table 1, homologs thereof, and orthologs thereof.

TABLE 1 SHH1 Proteins SED ID Organism Gene Name NO. Arabidopsis thalianaNP_849666.2 1 Ricinus communis XP_002515974.1 2 Glycine maxXP_003531650.1 3 Zea mays NP_001141052.1 4 Medicago truncatulaAFK39040.1 5 Physcomitrella patens XP_001760710.1 6 Sorghum bicolorXP_002462170.1 7 Oryza sativa NP_001062942.1 8 Brachypodium distachyonXP_003563870.1 9 Populus trichocarpa XP_002299736.1 10 Vitis viniferaXP_002283948.1 11 Cucumis sativus XP_004155951.1 12 Arabidopsis lyrataXP_002890094.1 13

In some embodiments, an SHH1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SHH1 protein (SEQ ID NO: 1).

An SHH1-like protein may include the amino acid sequence or a fragmentthereof of any SHH1 homolog or ortholog, such as any one of those listedin Table 1. One of skill would readily recognize that additional SHH1homologs and/or orthologs may exist and may be used herein.

SHH2 Proteins

Certain aspects of the present disclosure relate to SHH2-like proteins.In some embodiments, an SHH2-like protein refers to a recombinant SHH2protein or fragment thereof that contains a heterologous DNA-bindingdomain. In some embodiments, an SHH2-like protein refers to arecombinant SHH2 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an SHH2-like proteinrefers to a recombinant SHH2 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anSHH2-like protein refers to a recombinant SHH2 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. SHH2-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

SHH2 is a homolog of SHH1 as described above. In some embodiments,SHH2-like proteins of the present disclosure are chromatin-bindingproteins. In some embodiments, an SHH2-like protein of the presentdisclosure includes a functional fragment of a full-length SHH2 proteinwhere the fragment maintains the ability to recruit RNA Pol IV to DNA.In some embodiments, an SHH2 protein fragment contains at least 20consecutive amino acids, at least 30 consecutive amino acids, at least40 consecutive amino acids, at least 50 consecutive amino acids, atleast 60 consecutive amino acids, at least 70 consecutive amino acids,at least 80 consecutive amino acids, at least 90 consecutive aminoacids, at least 100 consecutive amino acids, at least 120 consecutiveamino acids, at least 140 consecutive amino acids, at least 160consecutive amino acids, at least 180 consecutive amino acids, at least200 consecutive amino acids, at least 220 consecutive amino acids, atleast 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length SHH2 protein. In some embodiments, SHH2 proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length SHH2 protein.In some embodiments, SHH2 protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-length SHH2protein. In some embodiments, SHH2 protein fragments may includesequences with one or more amino acids added to an otherwise consecutiveamino acid sequence of a full-length SHH2 protein.

Suitable SHH2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SHH2 proteins may include, for example, thoselisted in Table 2, homologs thereof, and orthologs thereof.

TABLE 2 SHH2 Proteins SED ID Organism Gene Name NO. Arabidopsis thalianaAEE76089 14

In some embodiments, an SHH2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SHH2 protein (SEQ ID NO: 14). Suitable SHH2 proteins may alsoinclude homologous SHH1 proteins, such as those described in Table 1.

An SHH2-like protein may include the amino acid sequence or a fragmentthereof of any SHH2 homolog or ortholog, such as any one of those listedin Table 2. One of skill would readily recognize that additional SHH2homologs and/or orthologs may exist and may be used herein.

AGO4 Proteins

Certain aspects of the present disclosure relate to AGO4-like proteins.In some embodiments, an AGO4-like protein refers to a recombinant AGO4protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an AGO4-like protein refers to arecombinant AGO4 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an AGO4-like proteinrefers to a recombinant AGO4 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anAGO4-like protein refers to a recombinant AGO4 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. AGO4-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

AGO4 proteins are known in the art and are described herein. In someembodiments, an AGO4 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length AGO4 protein. In some embodiments, AGO4 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length AGO4 protein. In someembodiments, AGO4 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length AGO4 protein. In someembodiments, AGO4 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length AGO4 protein.

Suitable AGO4 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable AGO4 proteins may include, for example, thoselisted in Table 3, homologs thereof, and orthologs thereof.

TABLE 3 AGO4 Proteins SED ID Organism Gene Name NO. Arabidopsis thalianaQ9ZVD5 15 Arabidopsis lyrata XP_002880875 16 Cucumis sativusXP_011653531 17 Vitis vinifera XP_002275928 18 Medicago truncatulaXP_003617095 19 Ricinus communis XP_002527764 20 Glycine maxXP_003545462 21 Zea mays NP_001167850 22 Sorghum bicolor XP_002440386 23Oryza sativa NP_001052115 24 Brachypodium distachyon XP_010230772 25Populus trichocarpa XP_006369390 26 Brassica napus CDX77061 27

In some embodiments, an AGO4 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana AGO4 protein (SEQ ID NO: 15).

An AGO4-like protein may include the amino acid sequence or a fragmentthereof of any AGO4 homolog or ortholog, such as any one of those listedin Table 3. One of skill would readily recognize that additional AGO4homologs and/or orthologs may exist and may be used herein.

AGO4 is a PAZ/PIWI domain-containing protein that belongs to a clade ofproteins that includes e.g. AGO6 and AGO9. Exemplary proteins in thisclade, using A. thaliana as an exemplary host plant, include, forexample, AGO6 (SEQ ID NO: 363) and AGO9 (SEQ ID NO: 364). An alignmentof various proteins in this clade from A. thaliana is provided inFIG. 1. The proteins in this clade, as well as homologs and orthologsthereof, may also be used in the methods and compositions of the presentdisclosure to target and silence a specific nucleic acid as describedherein for AGO4-like proteins. AGO3 (SEQ ID NO: 503), as well ashomologs and orthologs thereof, may also be used in the methods andcompositions of the present disclosure to target and silence a specificnucleic acid as described herein for AGO4-like proteins.

HDA6 Proteins

Certain aspects of the present disclosure relate to HDA6-like proteins.In some embodiments, an HDA6-like protein refers to a recombinant HDA6protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an HDA6-like protein refers to arecombinant HDA6 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an HDA6-like proteinrefers to a recombinant HDA6 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anHDA6-like protein refers to a recombinant HDA6 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. HDA6-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

HDA6 proteins are known in the art and are described herein. In someembodiments, an HDA6 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length HDA6 protein. In some embodiments, HDA6 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length HDA6 protein. In someembodiments, HDA6 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length HDA6 protein. In someembodiments, HDA6 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length HDA6 protein.

Suitable HDA6 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable HDA6 proteins may include, for example, thoselisted in Table 4, homologs thereof, and orthologs thereof.

TABLE 4 HDA6 Proteins SED ID Organism Gene Name NO. Arabidopsis thalianaQ9FML2 28 Arabidopsis lyrata XP_002866535 29 Cucumis sativusXP_004138094 30 Vitis vinifera XP_010663108 31 Medicago truncatulaXP_003601202 32 Ricinus communis XP_002511337 33 Glycine maxXP_003525556 34 Zea mays NP_001104901 35 Sorghum bicolor XP_002444249 36Oryza sativa NP_001061596 37 Brachypodium distachyon XP_003573796 38Populus trichocarpa XP_002322192 39 Brassica napus CDX84385 40

In some embodiments, an HDA6 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana HDA6 protein (SEQ ID NO: 28).

An HDA6-like protein may include the amino acid sequence or a fragmentthereof of any HDA6 homolog or ortholog, such as any one of those listedin Table 4. One of skill would readily recognize that additional HDA6homologs and/or orthologs may exist and may be used herein.

HDA6 is a histone deacetylase that belongs to a clade of proteins thatincludes e.g. HDA1, HDA7, and HDA9. Exemplary proteins in this clade,using A. thaliana as an exemplary host plant, include, for example, HDA1(SEQ ID NO: 365), HDA7 (SEQ ID NO: 366), HDA9 (SEQ ID NO: 367), HDA15(SEQ ID NO: 369), and HDA14 (SEQ ID NO: 370). An alignment of variousproteins in this clade from A. thaliana is provided in FIG. 2. Theproteins in this clade, as well as homologs and orthologs thereof, mayalso be used in the methods and compositions of the present disclosureto target and silence a specific nucleic acid as described herein forHDA6-like proteins.

NRPD1 Proteins

Certain aspects of the present disclosure relate to NRPD1-like proteins.In some embodiments, an NRPD1-like protein refers to a recombinant NRPD1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an NRPD1-like protein refers to arecombinant NRPD1 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an NRPD1-like proteinrefers to a recombinant NRPD1 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anNRPD1-like protein refers to a recombinant NRPD1 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.NRPD1-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

NRPD1 proteins are known in the art and are described herein. NRPD1proteins encode a large subunit of RNA Pol IV. In some embodiments, anNRPD1 protein fragment contains at least 20 consecutive amino acids, atleast 30 consecutive amino acids, at least 40 consecutive amino acids,at least 50 consecutive amino acids, at least 60 consecutive aminoacids, at least 70 consecutive amino acids, at least 80 consecutiveamino acids, at least 90 consecutive amino acids, at least 100consecutive amino acids, at least 120 consecutive amino acids, at least140 consecutive amino acids, at least 160 consecutive amino acids, atleast 180 consecutive amino acids, at least 200 consecutive amino acids,at least 220 consecutive amino acids, at least 240 consecutive aminoacids, or 241 or more consecutive amino acids of a full-length NRPD1protein. In some embodiments, NRPD1 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPD1 protein. In some embodiments,NRPD1 protein fragments may include sequences with one or more aminoacids replaced/substituted with an amino acid different from theendogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length NRPD1 protein. In someembodiments, NRPD1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPD1 protein.

Suitable NRPD1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPD1 proteins may include, for example, thoselisted in Table 5, homologs thereof, and orthologs thereof.

TABLE 5 NRPD1 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q9LQ02 41 Arabidopsis lyrata XP_002886441.1 42 Cucumis sativusXP_004147993 43 Vitis vinifera XP_010661369.1 44 Medicago truncatulaAES94122.2 45 Ricinus communis XP_002509696.1 46 Glycine maxXP_006573754.1 47 Zea mays NP_001182824.1 48 Sorghum bicolorXP_002446962 49 Oryza sativa EEE61535 50 Brachypodium distachyonXP_003566523.1 51 Populus trichocarpa XP_002298071.2 52 Brassica napusCDY32191 53

In some embodiments, an NRPD1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana NRPD1 protein (SEQ ID NO: 41).

An NRPD1-like protein may include the amino acid sequence or a fragmentthereof of any NRPD1 homolog or ortholog, such as any one of thoselisted in Table 5. One of skill would readily recognize that additionalNRPD1 homologs and/or orthologs may exist and may be used herein.

NRPE1 Proteins

Certain aspects of the present disclosure relate to NRPE1-like proteins.In some embodiments, an NRPE1-like protein refers to a recombinant NRPE1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an NRPE1-like protein refers to arecombinant NRPE1 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an NRPE1-like proteinrefers to a recombinant NRPE1 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anNRPE1-like protein refers to a recombinant NRPE1 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.NRPE1-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

NRPE1 proteins are known in the art and are described herein. NRPE1proteins encode a large subunit of RNA Pol V. In some embodiments, anNRPE1 protein fragment contains at least 20 consecutive amino acids, atleast 30 consecutive amino acids, at least 40 consecutive amino acids,at least 50 consecutive amino acids, at least 60 consecutive aminoacids, at least 70 consecutive amino acids, at least 80 consecutiveamino acids, at least 90 consecutive amino acids, at least 100consecutive amino acids, at least 120 consecutive amino acids, at least140 consecutive amino acids, at least 160 consecutive amino acids, atleast 180 consecutive amino acids, at least 200 consecutive amino acids,at least 220 consecutive amino acids, at least 240 consecutive aminoacids, or 241 or more consecutive amino acids of a full-length NRPE1protein. In some embodiments, NRPE1 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPE1 protein. In some embodiments,NRPE1 protein fragments may include sequences with one or more aminoacids replaced/substituted with an amino acid different from theendogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length NRPE1 protein. In someembodiments, NRPE1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPE1 protein.

Suitable NRPE1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPE1 proteins may include, for example, thoselisted in Table 6, homologs thereof, and orthologs thereof.

TABLE 6 NRPE1 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q5D869 54 Arabidopsis lyrata XP_002879839.1 55 Cucumis sativusXP_004155767.1 56 Vitis vinifera CBI40152.3 57 Medicago truncatulaAET02314.2 58 Ricinus communis XP_002513060 59 Glycine maxXP_006598109.1 60 Zea mays XP_008679943 61 Sorghum bicolorXP_002459158.1 62 Oryza sativa EEE56320 63 Brachypodium distachyonXP_010238829 64 Populus trichocarpa XP_002303926 65 Brassica napusCDY60335 66

In some embodiments, an NRPE1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana NRPE1 protein (SEQ ID NO: 54).

An NRPE1-like protein may include the amino acid sequence or a fragmentthereof of any NRPE1 homolog or ortholog, such as any one of thoselisted in Table 6. One of skill would readily recognize that additionalNRPE1 homologs and/or orthologs may exist and may be used herein.

In addition to the NRPE1 proteins, orthologs, and homologs describedherein, NRPE1 proteins contain a domain known as the AGO hook, which isinvolved with binding AGO4 proteins. Exemplary sequences of the AGOhook, using A. thaliana as an exemplary host plant, include, forexample, SEQ ID NO: 371. An exemplary polypeptide containing a 5×multimerized AGO-hook is presented in SEQ ID NO: 372. Proteins andprotein fragments containing an AGO-hook sequence may also be used inthe methods and compositions of the present disclosure to target andsilence a specific nucleic acid as described herein for NRPE1-likeproteins.

JMJ14 Proteins

Certain aspects of the present disclosure relate to JMJ14-like proteins.In some embodiments, a JMJ14-like protein refers to a recombinant JMJ14protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a JMJ14-like protein refers to arecombinant JMJ14 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a JMJ14-like proteinrefers to a recombinant JMJ14 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aJMJ14-like protein refers to a recombinant JMJ14 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.JMJ14-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

JMJ14 proteins are known in the art and are described herein. In someembodiments, a JMJ14 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length JMJ14 protein. In some embodiments, JMJ14 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length JMJ14 protein. In someembodiments, JMJ14 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length JMJ14 protein. In someembodiments, JMJ14 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length JMJ14 protein.

Suitable JMJ14 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable JMJ14 proteins may include, for example, thoselisted in Table 7, homologs thereof, and orthologs thereof.

TABLE 7 JMJ14 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q8GUI6 80 Arabidopsis lyrata XP_002869932 81 Cucumis sativusXP_004135564 82 Vitis vinifera CBI39010 83 Medicago truncatula KEH3777884 Ricinus communis XP_002529883 85 Glycine max XP_003535005 86 Zea maysXP_008648146 87 Sorghum bicolor XP_002454748 88 Oryza sativa EEE63155 89Brachypodium distachyon XP_010235272 90 Populus trichocarpa XP_00637048491 Brassica napus CDX82762 92

In some embodiments, a JMJ14 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana JMJ14 protein (SEQ ID NO: 80).

A JMJ14-like protein may include the amino acid sequence or a fragmentthereof of any JMJ14 homolog or ortholog, such as any one of thoselisted in Table 7. One of skill would readily recognize that additionalJMJ14 homologs and/or orthologs may exist and may be used herein.

JMJ14 is an H3K4 demethylase that belongs to a clade of proteins thatincludes e.g. JMJ18, JMJ15, and PKDM7D. Exemplary proteins in thisclade, using A. thaliana as an exemplary host plant, include, forexample, JMJ18 (SEQ ID NO: 376), JMJ15 (SEQ ID NO: 377), and PKDM7D (SEQID NO: 378). An alignment of various proteins in this clade from A.thaliana is provided in FIG. 3A-3B. The proteins in this clade, as wellas homologs and orthologs thereof, may also be used in the methods andcompositions of the present disclosure to target and silence a specificnucleic acid as described herein for JMJ14-like proteins.

RDR2 Proteins

Certain aspects of the present disclosure relate to RDR2-like proteins.In some embodiments, an RDR2-like protein refers to a recombinant RDR2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an RDR2-like protein refers to arecombinant RDR2 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an RDR2-like proteinrefers to a recombinant RDR2 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anRDR2-like protein refers to a recombinant RDR2 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. RDR2-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

RDR2 proteins are known in the art and are described herein. In someembodiments, a RDR2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length RDR2 protein. In some embodiments, RDR2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length RDR2 protein. In someembodiments, RDR2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length RDR2 protein. In someembodiments, RDR2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length RDR2 protein.

Suitable RDR2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable RDR2 proteins may include, for example, thoselisted in Table 8, homologs thereof, and orthologs thereof.

TABLE 8 RDR2 Proteins SED ID Organism Gene Name NO. Arabidopsis thalianaO82504 132 Arabidopsis lyrata XP_002872551 133 Cucumis sativusNP_001267608 134 Vitis vinifera XP_002280099 135 Medicago truncatulaKEH31853 136 Ricinus communis XP_002511431 137 Glycine max XP_006579560138 Zea mays NP_001183867 139 Sorghum bicolor XP_002446635 140 Oryzasativa EEE57765 141 Brachypodium disiachyon XP_003579930 142 Populustrichocarpa XP_002321582 143 Brassica napus CDX86814 144

In some embodiments, an RDR2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana RDR2 protein (SEQ ID NO: 132).

An RDR2-like protein may include the amino acid sequence or a fragmentthereof of any RDR2 homolog or ortholog, such as any one of those listedin Table 8. One of skill would readily recognize that additional RDR2homologs and/or orthologs may exist and may be used herein.

RDR2 is an RNA-dependent RNA polymerase and forms a complex with RNA PolIV. RDR2 belongs to a clade of proteins that includes e.g. RDR1.Exemplary proteins in this clade, using A. thaliana as an exemplary hostplant, include, for example, RDR1 (SEQ ID NO: 389). An alignment ofvarious proteins in this clade from A. thaliana is provided in FIG.4A-4B. The proteins in this clade, as well as homologs and orthologsthereof, may also be used in the methods and compositions of the presentdisclosure to target and silence a specific nucleic acid as describedherein for RDR2-like proteins.

NRPD2A/NRPE2 Proteins

Certain aspects of the present disclosure relate to NRPD2A/NRPE2-likeproteins. In some embodiments, an NRPD2A/NRPE2-like protein refers to arecombinant NRPD2A/NRPE2 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPD2A/NRPE2-like protein refers to a recombinant NRPD2A/NRPE2 proteinor fragment thereof that is fused to a CAS9 protein or fragment thereof.In some embodiments, an NRPD2A/NRPE2-like protein refers to arecombinant NRPD2A/NRPE2 protein or fragment thereof that is fused to anMS2 coat protein or fragment thereof. In some embodiments, anNRPD2A/NRPE2-like protein refers to a recombinant NRPD2A/NRPE2 proteinor fragment thereof that is fused to an scFV antibody or fragmentthereof. NRPD2A/NRPE2-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

NRPD2A/NRPE2 proteins are known in the art and are described herein.NRPD2A and NRPE2 are alternative names for the same protein, as isreadily understood in the art. NRPD2A/NRPE2 proteins encode a subunit ofRNA Pol IV. In some embodiments, an NRPD2A/NRPE2 protein fragmentcontains at least 20 consecutive amino acids, at least 30 consecutiveamino acids, at least 40 consecutive amino acids, at least 50consecutive amino acids, at least 60 consecutive amino acids, at least70 consecutive amino acids, at least 80 consecutive amino acids, atleast 90 consecutive amino acids, at least 100 consecutive amino acids,at least 120 consecutive amino acids, at least 140 consecutive aminoacids, at least 160 consecutive amino acids, at least 180 consecutiveamino acids, at least 200 consecutive amino acids, at least 220consecutive amino acids, at least 240 consecutive amino acids, or 241 ormore consecutive amino acids of a full-length NRPD2A/NRPE2 protein. Insome embodiments, NRPD2A/NRPE2 protein fragments may include sequenceswith one or more amino acids removed from the consecutive amino acidsequence of a full-length NRPD2A/NRPE2 protein. In some embodiments,NRPD2A/NRPE2 protein fragments may include sequences with one or moreamino acids replaced/substituted with an amino acid different from theendogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length NRPD2A/NRPE2 protein.In some embodiments, NRPD2A/NRPE2 protein fragments may includesequences with one or more amino acids added to an otherwise consecutiveamino acid sequence of a full-length NRPD2A/NRPE2 protein.

Suitable NRPD2A/NRPE2 proteins may be identified and isolated frommonocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPD2A/NRPE2 proteins may include, forexample, those listed in Table 9, homologs thereof, and orthologsthereof.

TABLE 9 NRPD2A/NRPE2 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q9LK40 145 Arabidopsis lyrata XP_002883108.1 146 Cucumissativus XP_004145500.1 147 Vitis vinifera CBI21137.3 148 Medicagotruncatula AES73546.2 149 Ricinus communis XP_002515428.1 150 Glycinemax XP_003523670.1 151 Zea mays NP_001177299 152 Sorghum bicolorXP_002468227 153 Oryza sativa NP_001054041 154 Brachypodium distachyonXP_003577435.2 155 Populus trichocarpa XP_002324332.2 156 Brassica napusCDX92193 157

In some embodiments, an NRPD2A/NRPE2 protein or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofthe A. thaliana NRPD2A/NRPE2 protein (SEQ ID NO: 145).

An NRPD2A/NRPE2-like protein may include the amino acid sequence or afragment thereof of any NRPD2A/NRPE2 homolog or ortholog, such as anyone of those listed in Table 9. One of skill would readily recognizethat additional NRPD2A/NRPE2 homologs and/or orthologs may exist and maybe used herein.

NRPB3/NRPD3/NRPE3A Proteins

Certain aspects of the present disclosure relate toNRPB3/NRPD3/NRPE3A-like proteins. In some embodiments, anNRPB3/NRPD3/NRPE3A-like protein refers to a recombinantNRPB3/NRPD3/NRPE3A protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB3/NRPD3/NRPE3A-like protein refers to a recombinantNRPB3/NRPD3/NRPE3A protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB3/NRPD3/NRPE3A-like protein refers to a recombinantNRPB3/NRPD3/NRPE3A protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB3/NRPD3/NRPE3A-like protein refers to a recombinantNRPB3/NRPD3/NRPE3A protein or fragment thereof that is fused to an scFVantibody or fragment thereof. NRPB3/NRPD3/NRPE3A-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

NRPB3/NRPD3/NRPE3A proteins are known in the art and are describedherein. NRPB3, NRPD3, and NRPE3A are alternative names for the sameprotein, as is readily understood in the art. NRPB3/NRPD3/NRPE3Aproteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB3/NRPD3/NRPE3A protein fragment contains at least 20consecutive amino acids, at least 30 consecutive amino acids, at least40 consecutive amino acids, at least 50 consecutive amino acids, atleast 60 consecutive amino acids, at least 70 consecutive amino acids,at least 80 consecutive amino acids, at least 90 consecutive aminoacids, at least 100 consecutive amino acids, at least 120 consecutiveamino acids, at least 140 consecutive amino acids, at least 160consecutive amino acids, at least 180 consecutive amino acids, at least200 consecutive amino acids, at least 220 consecutive amino acids, atleast 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB3/NRPD3/NRPE3A protein. In some embodiments,NRPB3/NRPD3/NRPE3A protein fragments may include sequences with one ormore amino acids removed from the consecutive amino acid sequence of afull-length NRPB3/NRPD3/NRPE3A protein. In some embodiments,NRPB3/NRPD3/NRPE3A protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length NRPB3/NRPD3/NRPE3Aprotein. In some embodiments, NRPB3/NRPD3/NRPE3A protein fragments mayinclude sequences with one or more amino acids added to an otherwiseconsecutive amino acid sequence of a full-length NRPB3/NRPD3/NRPE3Aprotein.

Suitable NRPB3/NRPD3/NRPE3A proteins may be identified and isolated frommonocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB3/NRPD3/NRPE3A proteins may include,for example, those listed in Table 10, homologs thereof, and orthologsthereof.

TABLE 10 NRPB3/NRPD3/NRPE3A Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q39211 158 Arabidopsis lyrata XP_002883895 159Cucumis sativus XP_004138895 160 Vitis vinifera CAN60923 161 Medicagotruncatula XP_003607895 162 Ricinus communis XP_002518700 163 Glycinemax XP_003529425 164 Zea mays NP_001149261 165 Sorghum bicolorXP_002462055 166 Oryza sativa NP_001062572 167 Brachypodium distachyonXP_003576823 168 Populus trichocarpa XP_002313865 169 Brassica napusCDY62312 170

In some embodiments, an NRPB3/NRPD3/NRPE3A protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB3/NRPD3/NRPE3A protein (SEQ ID NO: 158).

An NRPB3/NRPD3/NRPE3A-like protein may include the amino acid sequenceor a fragment thereof of any NRPB3/NRPD3/NRPE3A homolog or ortholog,such as any one of those listed in Table 10. One of skill would readilyrecognize that additional NRPB3/NRPD3/NRPE3A homologs and/or orthologsmay exist and may be used herein.

NRPE3B Proteins

Certain aspects of the present disclosure relate to NRPE3B-likeproteins. In some embodiments, an NRPE3B-like protein refers to arecombinant NRPE3B protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, an NRPE3B-likeprotein refers to a recombinant NRPE3B protein or fragment thereof thatis fused to a CAS9 protein or fragment thereof. In some embodiments, anNRPE3B-like protein refers to a recombinant NRPE3B protein or fragmentthereof that is fused to an MS2 coat protein or fragment thereof. Insome embodiments, an NRPE3B-like protein refers to a recombinant NRPE3Bprotein or fragment thereof that is fused to an scFV antibody orfragment thereof. NRPE3B-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

NRPE3B proteins are known in the art and are described herein. NRPE3Bproteins encode a subunit of RNA Pol V. In some embodiments, an NRPE3Bprotein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPE3B protein.In some embodiments, NRPE3B protein fragments may include sequences withone or more amino acids removed from the consecutive amino acid sequenceof a full-length NRPE3B protein. In some embodiments, NRPE3B proteinfragments may include sequences with one or more amino acidsreplaced/substituted with an amino acid different from the endogenousamino acid present at a given amino acid position in a consecutive aminoacid sequence of a full-length NRPE3B protein. In some embodiments,NRPE3B protein fragments may include sequences with one or more aminoacids added to an otherwise consecutive amino acid sequence of afull-length NRPE3B protein.

Suitable NRPE3B proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPE3B proteins may include, for example, thoselisted in Table 11, homologs thereof, and orthologs thereof.

TABLE 11 NRPE3B Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q39212 171 Arabidopsis lyrata XP_002883894 172 Cucumis sativusXP_004138895 173 Vitis vinifera CAN60923 174 Medicago truncatulaXP_003607895 175 Ricinus communis XP_002518700 176 Glycine maxXP_003529425 177 Zea mays NP_001149261 178 Sorghum bicolor XP_002462055179 Oryza sativa XP_002960614 180 Brachypodium distachyon XP_003576823181 Populus trichocarpa XP_002313865 182 Brassica napus CDY62312 183

In some embodiments, an NRPE3B protein or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofthe A. thaliana NRPE3B protein (SEQ ID NO: 171).

An NRPE3B-like protein may include the amino acid sequence or a fragmentthereof of any NRPE3B homolog or ortholog, such as any one of thoselisted in Table 11. One of skill would readily recognize that additionalNRPE3B homologs and/or orthologs may exist and may be used herein.

NRPB11/NRPD11/NRPE11 Proteins

Certain aspects of the present disclosure relate toNRPB11/NRPD11/NRPE11-like proteins. In some embodiments, anNRPB11/NRPD11/NRPE11-like protein refers to a recombinantNRPB11/NRPD11/NRPE11 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB11/NRPD11/NRPE11-like protein refers to a recombinantNRPB11/NRPD11/NRPE11 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB11/NRPD11/NRPE11-like protein refers to a recombinantNRPB11/NRPD11/NRPE11 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB1/NRPD11/NRPE11-like protein refers to a recombinantNRPB11/NRPD11/NRPE11 protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB11/NRPD11/NRPE11-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB11/NRPD11/NRPE11 proteins are known in the art and are describedherein. NRPB11, NRPD11, and NRPE11 are alternative names for the sameprotein, as is readily understood in the art. NRPB11/NRPD11/NRPE11proteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB11/NRPD11/NRPE11 protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB11/NRPD11/NRPE11 protein. In someembodiments, NRPB11/NRPD11/NRPE11 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB11/NRPD11/NRPE11 protein. Insome embodiments, NRPB11/NRPD11/NRPE11 protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB11/NRPD11/NRPE11 protein. In some embodiments,NRPB11/NRPD11/NRPE11 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB11/NRPD11/NRPE11 protein.

Suitable NRPB11/NRPD11/NRPE11 proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB11/NRPD11/NRPE11 proteins may include,for example, those listed in Table 12, homologs thereof, and orthologsthereof.

TABLE 12 NRPB11/NRPD11/NRPE11 Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana F4J5R0 184 Arabidopsis lyrata XP_002877842 185Cucumis sativus XP_004149719 186 Vitis vinifera CAN70445 187 Medicagotruncatula KEH24769 188 Ricinus communis XP_002517812 189 Glycine maxXP_003534400 190 Zea mays XP_008681546 191 Sorghum bicolor XP_002447457192 Oryza sativa NP_001058998 193 Brachypodium distachyon XP_003578343194 Populus trichocarpa XP_002313254 195 Brassica napus CDY60635 196

In some embodiments, an NRPB11/NRPD11/NRPE11 protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB11/NRPD11/NRPE11 protein (SEQ ID NO:184).

An NRPB11/NRPD11/NRPE11-like protein may include the amino acid sequenceor a fragment thereof of any NRPB11/NRPD11/NRPE11 homolog or ortholog,such as any one of those listed in Table 12. One of skill would readilyrecognize that additional NRPB11/NRPD11/NRPE11 homologs and/or orthologsmay exist and may be used herein.

NRPB10/NRPD10/NRPE10 Proteins

Certain aspects of the present disclosure relate toNRPB10/NRPD10/NRPE10-like proteins. In some embodiments, anNRPB10/NRPD10/NRPE10-like protein refers to a recombinantNRPB10/NRPD10/NRPE10 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB10/NRPD10/NRPE10-like protein refers to a recombinantNRPB10/NRPD10/NRPE10 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB10/NRPD10/NRPE10-like protein refers to a recombinantNRPB10/NRPD10/NRPE10 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB10/NRPD10/NRPE10-like protein refers to a recombinantNRPB10/NRPD10/NRPE10 protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB10/NRPD10/NRPE10-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB10/NRPD10/NRPE10 proteins are known in the art and are describedherein. NRPB10, NRPD10, and NRPE10 are alternative names for the sameprotein, as is readily understood in the art. NRPB10/NRPD10/NRPE10proteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB10/NRPD10/NRPE10 protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB10/NRPD10/NRPE10 protein. In someembodiments, NRPB10/NRPD10/NRPE10 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB10/NRPD10/NRPE10 protein. Insome embodiments, NRPB10/NRPD10/NRPE10 protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB10/NRPD10/NRPE10 protein. In some embodiments,NRPB10/NRPD10/NRPE10 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB10/NRPD10/NRPE10 protein.

Suitable NRPB10/NRPD10/NRPE10 proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB10/NRPD10/NRPE10 proteins may include,for example, those listed in Table 13, homologs thereof, and orthologsthereof.

TABLE 13 NRPB10/NRPD10/NRPE10 Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q8LFJ6 197 Cucumis sativus XP_004135479 198 Vitisvinifera XP_002263065 199 Medicago truncatula XP_003613211 200 Ricinuscommunis XP_002532739 201 Glycine max XP_003517695 202 Zea maysNP_001149707 203 Sorghum bicolor XP_002449154 204 Oryza sativaNP_001066312 205 Brachypodium distachyon XP_003578831 206 Populustrichocarpa XP_002303467 207 Brassica napus CDY25312 208

In some embodiments, an NRPB10/NRPD10/NRPE10 protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB10/NRPD10/NRPE10 protein (SEQ ID NO:197).

An NRPB10/NRPD10/NRPE10-like protein may include the amino acid sequenceor a fragment thereof of any NRPB10/NRPD10/NRPE10 homolog or ortholog,such as any one of those listed in Table 13. One of skill would readilyrecognize that additional NRPB0/NRPD10/NRPE10 homologs and/or orthologsmay exist and may be used herein.

NRPB12/NRPD12/NRPE12 Proteins

Certain aspects of the present disclosure relate toNRPB12/NRPD12/NRPE12-like proteins. In some embodiments, anNRPB12/NRPD12/NRPE12-like protein refers to a recombinantNRPB12/NRPD12/NRPE12 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB12/NRPD12/NRPE12-like protein refers to a recombinantNRPB12/NRPD12/NRPE12 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB12/NRPD12/NRPE12-like protein refers to a recombinantNRPB12/NRPD12/NRPE12 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB12/NRPD12/NRPE12-like protein refers to a recombinantNRPB12/NRPD12/NRPE12 protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB12/NRPD12/NRPE12-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB12/NRPD12/NRPE12 proteins are known in the art and are describedherein. NRPB12, NRPD12, and NRPE12 are alternative names for the sameprotein, as is readily understood in the art. NRPB12/NRPD12/NRPE12proteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB12/NRPD12/NRPE12 protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB12/NRPD12/NRPE12 protein. In someembodiments, NRPB12/NRPD12/NRPE12 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB12/NRPD12/NRPE12 protein. Insome embodiments, NRPB12/NRPD12/NRPE12 protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB12/NRPD12/NRPE12 protein. In some embodiments,NRPB12/NRPD12/NRPE12 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB12/NRPD12/NRPE12 protein.

Suitable NRPB12/NRPD12/NRPE12 proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, and Oryza sativa. Examplesof suitable NRPB12/NRPD12/NRPE12 proteins may include, for example,those listed in Table 14, homologs thereof, and orthologs thereof.

TABLE 14 NRPB12/NRPD12/NRPE12 Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q9FLM8 209 Arabidopsis lyrata XP_002870659 210Cucumis sativus KGN64215 211 Vitis vinifera XP_010662206 212 Medicagotruncatula AFK41236 213 Ricinus communis XP_002527516 214 Glycine maxXP_003534102 215 Zea mays ACG30756 216 Oryza sativa NP_001172391 217Brachypodium distachyon XP_003563174 218 Populus trichocarpaXP_002317630 219 Brassica napus CDY24079 220

In some embodiments, an NRPB12/NRPD12/NRPE12 protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB12/NRPD12/NRPE12 protein (SEQ ID NO:209).

An NRPB12/NRPD12/NRPE12-like protein may include the amino acid sequenceor a fragment thereof of any NRPB12/NRPD12/NRPE12 homolog or ortholog,such as any one of those listed in Table 14. One of skill would readilyrecognize that additional NRPB12/NRPD12/NRPE12 homologs and/or orthologsmay exist and may be used herein.

NRPB6A/NRPD6A/NRPE6A Proteins

Certain aspects of the present disclosure relate toNRPB6A/NRPD6A/NRPE6A-like proteins. In some embodiments, anNRPB6A/NRPD6A/NRPE6A-like protein refers to a recombinantNRPB6A/NRPD6A/NRPE6A protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB6A/NRPD6A/NRPE6A-like protein refers to a recombinantNRPB6A/NRPD6A/NRPE6A protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB6A/NRPD6A/NRPE6A-like protein refers to a recombinantNRPB6A/NRPD6A/NRPE6A protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB6A/NRPD6A/NRPE6A-like protein refers to a recombinantNRPB6A/NRPD6A/NRPE6A protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB6A/NRPD6A/NRPE6A-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB6A/NRPD6A/NRPE6A proteins are known in the art and are describedherein. NRPB6A, NRPD6A, and NRPE6A are alternative names for the sameprotein, as is readily understood in the art. NRPB6A/NRPD6A/NRPE6Aproteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB6A/NRPD6A/NRPE6A protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB6A/NRPD6A/NRPE6A protein. In someembodiments, NRPB6A/NRPD6A/NRPE6A protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB6A/NRPD6A/NRPE6A protein. Insome embodiments, NRPB6A/NRPD6A/NRPE6A protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB6A/NRPD6A/NRPE6A protein. In some embodiments,NRPB6A/NRPD6A/NRPE6A protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB6A/NRPD6A/NRPE6A protein.

Suitable NRPB6A/NRPD6A/NRPE6A proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB6A/NRPD6A/NRPE6A proteins may include,for example, those listed in Table 15, homologs thereof, and orthologsthereof.

TABLE 15 NRPB6A/NRPD6A/NRPE6A Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q9SJ96 221 Arabidopsis lyrata XP_002885765 222Cucumis sativus XP_004136357 223 Vitis vinifera XP_002282723 224Medicago truncatula XP_003625191 225 Ricinus communis XP_002510834 226Glycine max XP_003536478 227 Zea mays ACF83139 228 Sorghum bicolorXP_002459814 229 Oryza sativa NP_001050570 230 Brachypodium distachyonXP_003575153 231 Populus trichocarpa XP_002322450 232 Brassica napusCDY30291 233

In some embodiments, an NRPB6A/NRPD6A/NRPE6A protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB6A/NRPD6A/NRPE6A protein (SEQ ID NO:221).

An NRPB6A/NRPD6A/NRPE6A-like protein may include the amino acid sequenceor a fragment thereof of any NRPB6A/NRPD6A/NRPE6A homolog or ortholog,such as any one of those listed in Table 15. One of skill would readilyrecognize that additional NRPB6A/NRPD6A/NRPE6A homologs and/or orthologsmay exist and may be used herein.

NRPB6B/NRPD6B/NRPE6B Proteins

Certain aspects of the present disclosure relate toNRPB6B/NRPD6B/NRPE6B-like proteins. In some embodiments, anNRPB6B/NRPD6B/NRPE6B-like protein refers to a recombinantNRPB6B/NRPD6B/NRPE6B protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB6B/NRPD6B/NRPE6B-like protein refers to a recombinantNRPB6B/NRPD6B/NRPE6B protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB6B/NRPD6B/NRPE6B-like protein refers to a recombinantNRPB6B/NRPD6B/NRPE6B protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB6B/NRPD6B/NRPE6B-like protein refers to a recombinantNRPB6B/NRPD6B/NRPE6B protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB6B/NRPD6B/NRPE6B-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB6B/NRPD6B/NRPE6B proteins are known in the art and are describedherein. NRPB6B, NRPD6B, and NRPE6B are alternative names for the sameprotein, as is readily understood in the art. NRPB6B/NRPD6B/NRPE6Bproteins encode a subunit of RNA Polymerases II and V. In someembodiments, an NRPB6B/NRPD6B/NRPE6B protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB6B/NRPD6B/NRPE6B protein. In someembodiments, NRPB6B/NRPD6B/NRPE6B protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB6B/NRPD6B/NRPE6B protein. Insome embodiments, NRPB6B/NRPD6B/NRPE6B protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB6B/NRPD6B/NRPE6B protein. In some embodiments,NRPB6B/NRPD6B/NRPE6B protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB6B/NRPD6B/NRPE6B protein.

Suitable NRPB6B/NRPD6B/NRPE6B proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB6B/NRPD6B/NRPE6B proteins may include,for example, those listed in Table 16, homologs thereof, and orthologsthereof.

TABLE 16 NRPB6B/NRPD6B/NRPE6B Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q9SJ96 234 Arabidopsis lyrata XP_002885765 235Cucumis sativus XP_004140788 236 Vitis vinifera CAN62586 237 Medicagotruncatula KEH17383 238 Ricinus communis XP_002510834 239 Glycine maxXP_003536478 240 Zea mays ACG24540 241 Sorghum bicolor XP_002459814 242Oryza sativa NP_001050570 243 Brachypodium distachyon XP_003575153 244Populus trichocarpa XP_002322450 245 Brassica napus CDY30291 246

In some embodiments, an NRPB6B/NRPD6B/NRPE6B protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB6B/NRPD6B/NRPE6B protein (SEQ ID NO:234).

An NRPB6B/NRPD6B/NRPE6B-like protein may include the amino acid sequenceor a fragment thereof of any NRPB6B/NRPD6B/NRPE6B homolog or ortholog,such as any one of those listed in Table 16. One of skill would readilyrecognize that additional NRPB6B/NRPD6B/NRPE6B homologs and/or orthologsmay exist and may be used herein.

NRPB8A/NRPE8A Proteins

Certain aspects of the present disclosure relate to NRPB8A/NRPE8A-likeproteins. In some embodiments, an NRPB8A/NRPE8A-like protein refers to arecombinant NRPB8A/NRPE8A protein or fragment thereof and that containsa heterologous DNA-binding domain. In some embodiments, anNRPB8A/NRPE8A-like protein refers to a recombinant NRPB8A/NRPE8A proteinor fragment thereof that is fused to a CAS9 protein or fragment thereof.In some embodiments, an NRPB8A/NRPE8A-like protein refers to arecombinant NRPB8A/NRPE8A protein or fragment thereof that is fused toan MS2 coat protein or fragment thereof. In some embodiments, anNRPB8A/NRPE8A-like protein refers to a recombinant NRPB8A/NRPE8A proteinor fragment thereof that is fused to an scFV antibody or fragmentthereof. NRPB8A/NRPE8A-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

NRPB8A/NRPE8A proteins are known in the art and are described herein.NRPB8A and NRPE8A are alternative names for the same protein, as isreadily understood in the art. NRPB8A/NRPE8A proteins encode a subunitof RNA Polymerases II and V. In some embodiments, an NRPB8A/NRPE8Aprotein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPB8A/NRPE8Aprotein. In some embodiments, NRPB8A/NRPE8A protein fragments mayinclude sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length NRPB8A/NRPE8A protein.In some embodiments, NRPB8A/NRPE8A protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB8A/NRPE8A protein. In some embodiments, NRPB8A/NRPE8Aprotein fragments may include sequences with one or more amino acidsadded to an otherwise consecutive amino acid sequence of a full-lengthNRPB8A/NRPE8A protein.

Suitable NRPB8A/NRPE8A proteins may be identified and isolated frommonocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB8A/NRPE8A proteins may include, forexample, those listed in Table 17, homologs thereof, and orthologsthereof.

TABLE 17 NRPB8A/NRPE8A Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana O81097 247 Arabidopsis lyrata XP_002891800 248Cucumis sativus XP_004149143 249 Vitis vinifera CAN73856 250 Medicagotruncatula AFK42881 251 Ricinus communis XP_002530308 252 Glycine maxNP_001237035 253 Zea mays NP_001147399 254 Sorghum bicolor XP_002466106255 Oryza sativa NP_001051880 256 Brachypodium distachyon XP_010227253257 Populus trichocarpa XP_006376377 258 Brassica rapa XP_009116628 259

In some embodiments, an NRPB8A/NRPE8A protein or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofthe A. thaliana NRPB8A/NRPE8A protein (SEQ ID NO: 247).

An NRPB8A/NRPE8A-like protein may include the amino acid sequence or afragment thereof of any NRPB8A/NRPE8A homolog or ortholog, such as anyone of those listed in Table 17. One of skill would readily recognizethat additional NRPB8A/NRPE8A homologs and/or orthologs may exist andmay be used herein.

NRPB8B/NRPD8B/NRPE8B Proteins

Certain aspects of the present disclosure relate toNRPB8B/NRPD8B/NRPE8B-like proteins. In some embodiments, anNRPB8B/NRPD8B/NRPE8B-like protein refers to a recombinantNRPB8B/NRPD8B/NRPE8B protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB8B/NRPD8B/NRPE8B-like protein refers to a recombinantNRPB8B/NRPD8B/NRPE8B protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB8B/NRPD8B/NRPE8B-like protein refers to a recombinantNRPB8B/NRPD8B/NRPE8B protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB8B/NRPD8B/NRPE8B-like protein refers to a recombinantNRPB8B/NRPD8B/NRPE8B protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB8B/NRPD8B/NRPE8B-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB8B/NRPD8B/NRPE8B proteins are known in the art and are describedherein. NRPB8B, NRPD8B, and NRPE8B are alternative names for the sameprotein, as is readily understood in the art. NRPB8B/NRPD8B/NRPE8Bproteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB8B/NRPD8B/NRPE8B protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB8B/NRPD8B/NRPE8B protein. In someembodiments, NRPB8B/NRPD8B/NRPE8B protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB8B/NRPD8B/NRPE8B protein. Insome embodiments, NRPB8B/NRPD8B/NRPE8B protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB8B/NRPD8B/NRPE8B protein. In some embodiments,NRPB8B/NRPD8B/NRPE8B protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB8B/NRPD8B/NRPE8B protein.

Suitable NRPB8B/NRPD8B/NRPE8B proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB8B/NRPD8B/NRPE8B proteins may include,for example, those listed in Table 18, homologs thereof, and orthologsthereof.

TABLE 18 NRPB8B/NRPD8B/NRPE8B Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana O81097 260 Arabidopsis lyrata XP_002891800 261Cucumis sativus XP_004149143 262 Vitis vinifera CAN73856 263 Medicagotruncatula AFK42881 264 Ricinus communis XP_002530308 265 Glycine maxNP_001237035 266 Zea mays NP_001147399 267 Sorghum bicolor XP_002466106268 Oryza sativa NP_001051880 269 Brachypodium distachyon XP_010227253270 Populus trichocarpa XP_006376377 271 Brassica rapa XP_009116628 272

In some embodiments, an NRPB8B/NRPD8B/NRPE8B protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB8B/NRPD8B/NRPE8B protein (SEQ ID NO:260).

An NRPB8B/NRPD8B/NRPE8B-like protein may include the amino acid sequenceor a fragment thereof of any NRPB8B/NRPD8B/NRPE8B homolog or ortholog,such as any one of those listed in Table 18. One of skill would readilyrecognize that additional NRPB8B/NRPD8B/NRPE8B homologs and/or orthologsmay exist and may be used herein.

NRPE5 Proteins

Certain aspects of the present disclosure relate to NRPE5-like proteins.In some embodiments, an NRPE5-like protein refers to a recombinant NRPE5protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an NRPE5-like protein refers to arecombinant NRPE5 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an NRPE5-like proteinrefers to a recombinant NRPE5 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anNRPE5-like protein refers to a recombinant NRPE5 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.NRPE5-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

NRPE5 proteins are known in the art and are described herein. NRPE5proteins encode a subunit of RNA Pol V. In some embodiments, an NRPE5protein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPE5 protein.In some embodiments, NRPE5 protein fragments may include sequences withone or more amino acids removed from the consecutive amino acid sequenceof a full-length NRPE5 protein. In some embodiments, NRPE5 proteinfragments may include sequences with one or more amino acidsreplaced/substituted with an amino acid different from the endogenousamino acid present at a given amino acid position in a consecutive aminoacid sequence of a full-length NRPE5 protein. In some embodiments, NRPE5protein fragments may include sequences with one or more amino acidsadded to an otherwise consecutive amino acid sequence of a full-lengthNRPE5 protein.

Suitable NRPE5 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPE5 proteins may include, for example, thoselisted in Table 19, homologs thereof, and orthologs thereof.

TABLE 19 NRPE5 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q9M1J2 273 Arabidopsis lyrata XP_002876396.1 274 Cucumissativus XP_004136650.1 275 Vitis vinifera XP_003632734 276 Medicagotruncatula XP_003625033.1 277 Ricinus communis XP_002513077.1 278Glycine max NP_001236527.1 279 Zea mays ACG37268 280 Sorghum bicolorXP_002450250.1 281 Oryza sativa NP_001066119.1 282 Brachypodiumdistachyon XP_010237978.1 283 Populus trichocarpa XP_002323257.2 284Brassica napus CDX72073 285

In some embodiments, an NRPE5 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana NRPE5 protein (SEQ ID NO: 273).

An NRPE5-like protein may include the amino acid sequence or a fragmentthereof of any NRPE5 homolog or ortholog, such as any one of thoselisted in Table 19. One of skill would readily recognize that additionalNRPE5 homologs and/or orthologs may exist and may be used herein.

NRPD4/NRPE4 Proteins

Certain aspects of the present disclosure relate to NRPD4/NRPE4-likeproteins. In some embodiments, an NRPD4/NRPE4-like protein refers to arecombinant NRPD4/NRPE4 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPD4/NRPE4-like protein refers to a recombinant NRPD4/NRPE4 protein orfragment thereof that is fused to a CAS9 protein or fragment thereof. Insome embodiments, an NRPD4/NRPE4-like protein refers to a recombinantNRPD4/NRPE4 protein or fragment thereof that is fused to an MS2 coatprotein or fragment thereof. In some embodiments, an NRPD4/NRPE4-likeprotein refers to a recombinant NRPD4/NRPE4 protein or fragment thereofthat is fused to an scFV antibody or fragment thereof. NRPD4/NRPE4-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

NRPD4/NRPE4 proteins are known in the art and are described herein.NRPD4 and NRPE4 are alternative names for the same protein, as isreadily understood in the art. NRPD4/NRPE4 proteins encode a subunit ofRNA Polymerases IV and V. In some embodiments, an NRPD4/NRPE4 proteinfragment contains at least 20 consecutive amino acids, at least 30consecutive amino acids, at least 40 consecutive amino acids, at least50 consecutive amino acids, at least 60 consecutive amino acids, atleast 70 consecutive amino acids, at least 80 consecutive amino acids,at least 90 consecutive amino acids, at least 100 consecutive aminoacids, at least 120 consecutive amino acids, at least 140 consecutiveamino acids, at least 160 consecutive amino acids, at least 180consecutive amino acids, at least 200 consecutive amino acids, at least220 consecutive amino acids, at least 240 consecutive amino acids, or241 or more consecutive amino acids of a full-length NRPD4/NRPE4protein. In some embodiments, NRPD4/NRPE4 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPD4/NRPE4 protein. In someembodiments, NRPD4/NRPE4 protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-lengthNRPD4/NRPE4 protein. In some embodiments, NRPD4/NRPE4 protein fragmentsmay include sequences with one or more amino acids added to an otherwiseconsecutive amino acid sequence of a full-length NRPD4/NRPE4 protein.

Suitable NRPD4/NRPE4 proteins may be identified and isolated frommonocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPD4/NRPE4 proteins may include, forexample, those listed in Table 20, homologs thereof, and orthologsthereof.

TABLE 20 NRPD4/NRPE4 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana F4JKY1 286 Arabidopsis lyrata XP_002870197.1 287 Cucumissativus KGN49020.1 288 Vitis vinifera XP_010646234 289 Medicagotruncatula AFK45778.1 290 Ricinus communis XP_002525033.1 291 Glycinemax XP_003534990.1 292 Zea mays NP_001130236.1 293 Sorghum bicolorXP_002453184 294 Oryza sativa BAH01271.1 295 Brachypodiurn distachyonXP_010236010.1 296 Populus trichocarpa XP_006373571.1 297 Brassica napusCDY37333 298

In some embodiments, an NRPD4/NRPE4 protein or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofthe A. thaliana NRPD4/NRPE4 protein (SEQ ID NO: 286).

An NRPD4/NRPE4-like protein may include the amino acid sequence or afragment thereof of any NRPD4/NRPE4 homolog or ortholog, such as any oneof those listed in Table 20. One of skill would readily recognize thatadditional NRPD4/NRPE4 homologs and/or orthologs may exist and may beused herein.

NRPE7 Proteins

Certain aspects of the present disclosure relate to NRPE7-like proteins.In some embodiments, an NRPE7-like protein refers to a recombinant NRPE7protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an NRPE7-like protein refers to arecombinant NRPE7 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an NRPE7-like proteinrefers to a recombinant NRPE7 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anNRPE7-like protein refers to a recombinant NRPE7 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.NRPE7-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

NRPE7 proteins are known in the art and are described herein. NRPE7proteins encode a subunit of RNA Pol V. In some embodiments, an NRPE7protein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPE7 protein.In some embodiments, NRPE7 protein fragments may include sequences withone or more amino acids removed from the consecutive amino acid sequenceof a full-length NRPE7 protein. In some embodiments, NRPE7 proteinfragments may include sequences with one or more amino acidsreplaced/substituted with an amino acid different from the endogenousamino acid present at a given amino acid position in a consecutive aminoacid sequence of a full-length NRPE7 protein. In some embodiments, NRPE7protein fragments may include sequences with one or more amino acidsadded to an otherwise consecutive amino acid sequence of a full-lengthNRPE7 protein.

Suitable NRPE7 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPE7 proteins may include, for example, thoselisted in Table 21, homologs thereof, and orthologs thereof.

TABLE 21 NRPE7 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana A6QRA1 299 Arabidopsis lyrata XP_002868270.1 300 Cucumissativus XP_004150402.1 301 Vitis vinifera XP_002284221.1 302 Medicagotruncatula AFK37080.1 303 Ricinus communis XP_002522607.1 304 Glycinemax XP_006605321.1 305 Zea mays NP_001150375 306 Sorghum bicolorXP_002439325.1 307 Oryza sativa NP_001054703.1 308 Brachypodiumdistachyon XP_003568883.1 309 Populus trichocarpa XP_002312568.1 310Brassica napus CDY40821 311

In some embodiments, an NRPE7 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana NRPE7 protein (SEQ ID NO: 299).

An NRPE7-like protein may include the amino acid sequence or a fragmentthereof of any NRPE7 homolog or ortholog, such as any one of thoselisted in Table 21. One of skill would readily recognize that additionalNRPE7 homologs and/or orthologs may exist and may be used herein.

NRPD7 Proteins

Certain aspects of the present disclosure relate to NRPD7-like proteins.In some embodiments, an NRPD7-like protein refers to a recombinant NRPD7protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an NRPD7-like protein refers to arecombinant NRPD7 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an NRPD7-like proteinrefers to a recombinant NRPD7 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anNRPD7-like protein refers to a recombinant NRPD7 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.NRPD7-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

NRPD7 proteins are known in the art and are described herein. NRPD7proteins encode a subunit of RNA Pol IV. In some embodiments, an NRPD7protein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPD7 protein.In some embodiments, NRPD7 protein fragments may include sequences withone or more amino acids removed from the consecutive amino acid sequenceof a full-length NRPD7 protein. In some embodiments, NRPD7 proteinfragments may include sequences with one or more amino acidsreplaced/substituted with an amino acid different from the endogenousamino acid present at a given amino acid position in a consecutive aminoacid sequence of a full-length NRPD7 protein. In some embodiments, NRPD7protein fragments may include sequences with one or more amino acidsadded to an otherwise consecutive amino acid sequence of a full-lengthNRPD7 protein.

Suitable NRPD7 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable NRPD7 proteins may include, for example, thoselisted in Table 22, homologs thereof, and orthologs thereof.

TABLE 22 NRPD7 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana Q8LE42 312 Arabidopsis lyrata XP_002883384.1 313 Cucumissativus XP_004150402.1 314 Vitis vinifera XP_002284221.1 315 Medicagotruncatula AFK37080.1 316 Ricinus communis XP_002522607.1 317 Glycinemax XP_006605319.1 318 Zea mays NP_001150375 319 Sorghum bicolorXP_002439325 320 Oryza sativa EEC78737.1 321 Brachypodium distachyonXP_003568883 322 Populus trichocarpa XP_002312568 323 Brassica napusCDY40821 324

In some embodiments, an NRPD7 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana NRPD7 protein (SEQ ID NO: 312).

An NRPD7-like protein may include the amino acid sequence or a fragmentthereof of any NRPD7 homolog or ortholog, such as any one of thoselisted in Table 22. One of skill would readily recognize that additionalNRPD7 homologs and/or orthologs may exist and may be used herein.

NRPB5/NRPD5 Proteins

Certain aspects of the present disclosure relate to NRPB5/NRPD5-likeproteins. In some embodiments, an NRPB5/NRPD5-like protein refers to arecombinant NRPB5/NRPD5 protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB5/NRPD5-like protein refers to a recombinant NRPB5/NRPD5 protein orfragment thereof that is fused to a CAS9 protein or fragment thereof. Insome embodiments, an NRPB5/NRPD5-like protein refers to a recombinantNRPB5/NRPD5 protein or fragment thereof that is fused to an MS2 coatprotein or fragment thereof. In some embodiments, an NRPB5/NRPD5-likeprotein refers to a recombinant NRPB5/NRPD5 protein or fragment thereofthat is fused to an scFV antibody or fragment thereof. NRPB5/NRPD5-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

NRPB5/NRPD5 proteins are known in the art and are described herein.NRPB5 and NRPD5 are alternative names for the same protein, as isreadily understood in the art. NRPB5/NRPD5 proteins encode a subunit ofRNA Polymerases I, II, III, and IV. In some embodiments, an NRPB5/NRPD5protein fragment contains at least 20 consecutive amino acids, at least30 consecutive amino acids, at least 40 consecutive amino acids, atleast 50 consecutive amino acids, at least 60 consecutive amino acids,at least 70 consecutive amino acids, at least 80 consecutive aminoacids, at least 90 consecutive amino acids, at least 100 consecutiveamino acids, at least 120 consecutive amino acids, at least 140consecutive amino acids, at least 160 consecutive amino acids, at least180 consecutive amino acids, at least 200 consecutive amino acids, atleast 220 consecutive amino acids, at least 240 consecutive amino acids,or 241 or more consecutive amino acids of a full-length NRPB5/NRPD5protein. In some embodiments, NRPB5/NRPD5 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB5/NRPD5 protein. In someembodiments, NRPB5/NRPD5 protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-lengthNRPB5/NRPD5 protein. In some embodiments, NRPB5/NRPD5 protein fragmentsmay include sequences with one or more amino acids added to an otherwiseconsecutive amino acid sequence of a full-length NRPB5/NRPD5 protein.

Suitable NRPB5/NRPD5 proteins may be identified and isolated frommonocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB5/NRPD5 proteins may include, forexample, those listed in Table 23, homologs thereof, and orthologsthereof.

TABLE 23 NRPB5/NRPD5 Proteins SED ID Organism Gene Name NO. Arabidopsisthaliana O81098 325 Arabidopsis lyrata XP_002885498 326 Cucumis sativusXP_004148944 327 Vitis vinifera XP_002284107 328 Medicago truncatulaAFK41303 329 Ricinus communis XP_002514265 330 Glycine max NP_001238044331 Zea mays NP_001132429 332 Oryza sativa NP_001044564 333 Brachypodiumdistachyon XP_003564430 334 Populus trichocarpa XP_002323257 335Brassica napus CDY37407 336

In some embodiments, an NRPB5/NRPD5 protein or fragment thereof of thepresent disclosure has an amino acid sequence with at least about 20%,at least about 25%, at least about 30%, at least about 40%, at leastabout 50%, at least about 55%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 91%, at least about 92%,at least about 93%, at least about 94%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% amino acid identity to the amino acid sequence ofthe A. thaliana NRPB5/NRPD5 protein (SEQ ID NO: 325).

An NRPB5/NRPD5-like protein may include the amino acid sequence or afragment thereof of any NRPB5/NRPD5 homolog or ortholog, such as any oneof those listed in Table 23. One of skill would readily recognize thatadditional NRPB5/NRPD5 homologs and/or orthologs may exist and may beused herein.

NRPB9A/NRPD9A/NRPE9A Proteins

Certain aspects of the present disclosure relate toNRPB9A/NRPD9A/NRPE9A-like proteins. In some embodiments, anNRPB9A/NRPD9A/NRPE9A-like protein refers to a recombinantNRPB9A/NRPD9A/NRPE9A protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB9A/NRPD9A/NRPE9A-like protein refers to a recombinantNRPB9A/NRPD9A/NRPE9A protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB9A/NRPD9A/NRPE9A-like protein refers to a recombinantNRPB9A/NRPD9A/NRPE9A protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB9A/NRPD9A/NRPE9A-like protein refers to a recombinantNRPB9A/NRPD9A/NRPE9A protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB9A/NRPD9A/NRPE9A-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB9A/NRPD9A/NRPE9A proteins are known in the art and are describedherein. NRPB9A, NRPD9A, and NRPE9A are alternative names for the sameprotein, as is readily understood in the art. NRPB9A/NRPD9A/NRPE9Aproteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB9A/NRPD9A/NRPE9A protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB9A/NRPD9A/NRPE9A protein. In someembodiments, NRPB9A/NRPD9A/NRPE9A protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB9A/NRPD9A/NRPE9A protein. Insome embodiments, NRPB9A/NRPD9A/NRPE9A protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB9A/NRPD9A/NRPE9A protein. In some embodiments,NRPB9A/NRPD9A/NRPE9A protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB9A/NRPD9A/NRPE9A protein.

Suitable NRPB9A/NRPD9A/NRPE9A proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB9A/NRPD9A/NRPE9A proteins may include,for example, those listed in Table 24, homologs thereof, and orthologsthereof.

TABLE 24 NRPB9A/NRPD9A/NRPE9A Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q6NLH0 337 Arabidopsis lyrata XP_002883036 338Cucumis melo XP_008438942 339 Vitis vinifera XP_002276956 340 Medicagotruncatula XP_003594777 341 Ricinus communis XP_002519205 342 Glycinemax NP_001235803 343 Zea mays NP_001150634 344 Sorghum bicolorXP_002443356 345 Oryza sativa ABA98929 346 Brachypodium distachyonXP_003579291 347 Populus trichocarpa XP_002312337 348 Brassica napusCDX86852 349

In some embodiments, an NRPB9A/NRPD9A/NRPE9A protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB9A/NRPD9A/NRPE9A protein (SEQ ID NO:337).

An NRPB9A/NRPD9A/NRPE9A-like protein may include the amino acid sequenceor a fragment thereof of any NRPB9A/NRPD9A/NRPE9A homolog or ortholog,such as any one of those listed in Table 24. One of skill would readilyrecognize that additional NRPB9A/NRPD9A/NRPE9A homologs and/or orthologsmay exist and may be used herein.

NRPB9B/NRPD9B/NRPE9B Proteins

Certain aspects of the present disclosure relate toNRPB9B/NRPD9B/NRPE9B-like proteins. In some embodiments, anNRPB9B/NRPD9B/NRPE9B-like protein refers to a recombinantNRPB9B/NRPD9B/NRPE9B protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, anNRPB9B/NRPD9B/NRPE9B-like protein refers to a recombinantNRPB9B/NRPD9B/NRPE9B protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, anNRPB9B/NRPD9B/NRPE9B-like protein refers to a recombinantNRPB9B/NRPD9B/NRPE9B protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, anNRPB9B/NRPD9B/NRPE9B-like protein refers to a recombinantNRPB9B/NRPD9B/NRPE9B protein or fragment thereof that is fused to anscFV antibody or fragment thereof. NRPB9B/NRPD9B/NRPE9B-like proteinsmay be used in reducing the expression of one or more target nucleicacids, such as genes, in plants.

NRPB9B/NRPD9B/NRPE9B proteins are known in the art and are describedherein. NRPB9B, NRPD9B, and NRPE9B are alternative names for the sameprotein, as is readily understood in the art. NRPB9B/NRPD9B/NRPE9Bproteins encode a subunit of RNA Polymerases II, IV, and V. In someembodiments, an NRPB9B/NRPD9B/NRPE9B protein fragment contains at least20 consecutive amino acids, at least 30 consecutive amino acids, atleast 40 consecutive amino acids, at least 50 consecutive amino acids,at least 60 consecutive amino acids, at least 70 consecutive aminoacids, at least 80 consecutive amino acids, at least 90 consecutiveamino acids, at least 100 consecutive amino acids, at least 120consecutive amino acids, at least 140 consecutive amino acids, at least160 consecutive amino acids, at least 180 consecutive amino acids, atleast 200 consecutive amino acids, at least 220 consecutive amino acids,at least 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length NRPB9B/NRPD9B/NRPE9B protein. In someembodiments, NRPB9B/NRPD9B/NRPE9B protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length NRPB9B/NRPD9B/NRPE9B protein. Insome embodiments, NRPB9B/NRPD9B/NRPE9B protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length NRPB9B/NRPD9B/NRPE9B protein. In some embodiments,NRPB9B/NRPD9B/NRPE9B protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length NRPB9B/NRPD9B/NRPE9B protein.

Suitable NRPB9B/NRPD9B/NRPE9B proteins may be identified and isolatedfrom monocot and dicot plants. Examples of such plants may include, forexample, Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Medicago truncatula, Physcomitrella patens, Sorghum bicolor, and Oryzasativa. Examples of suitable NRPB9B/NRPD9B/NRPE9B proteins may include,for example, those listed in Table 25, homologs thereof, and orthologsthereof.

TABLE 25 NRPB9B/NRPD9B/NRPE9B Proteins SED ID Organism Gene Name NO.Arabidopsis thaliana Q8L5V0 350 Arabidopsis lyrata XP_002883036 351Cucumis melo XP_008438942 352 Vitis vinifera XP_002276956 353 Medicagotruncatula XP_003594777 354 Ricinus communis XP_002519205 355 Glycinemax NP_001235803 356 Zea mays NP_001150634 357 Sorghum bicolorXP_002443356 358 Oryza sativa ABA98929 359 Brachypodium distachyonXP_003559043 360 Populus trichocarpa XP_002312337 361 Brassica napusCDX99562 362

In some embodiments, an NRPB9B/NRPD9B/NRPE9B protein or fragment thereofof the present disclosure has an amino acid sequence with at least about20%, at least about 25%, at least about 30%, at least about 40%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%, at least about 95%, atleast about 96%, at least about 97%, at least about 98%, at least about99%, or at least about 100% amino acid identity to the amino acidsequence of the A. thaliana NRPB9B/NRPD9B/NRPE9B protein (SEQ ID NO:350).

An NRPB9B/NRPD9B/NRPE9B-like protein may include the amino acid sequenceor a fragment thereof of any NRPB9B/NRPD9B/NRPE9B homolog or ortholog,such as any one of those listed in Table 25. One of skill would readilyrecognize that additional NRPB9B/NRPD9B/NRPE9B homologs and/or orthologsmay exist and may be used herein.

SUVH2 Proteins

Certain aspects of the present disclosure relate to SUVH2-like proteins.In some embodiments, a SUVH2-like protein refers to a recombinant SUVH2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a SUVH2-like protein refers to arecombinant SUVH2 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a SUVH2-like proteinrefers to a recombinant SUVH2 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aSUVH2-like protein refers to a recombinant SUVH2 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.SUVH2-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

SUVH2 proteins are known in the art and are described herein. In someembodiments, a SUVH2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length SUVH2 protein. In some embodiments, SUVH2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length SUVH2 protein. In someembodiments, SUVH2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVH2 protein. In someembodiments, SUVH2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVH2 protein.

Suitable SUVH2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVH2 proteins may include, for example, thoselisted in Table 26, homologs thereof, and orthologs thereof.

TABLE 26 SUVH2 Proteins SEQ ID Organism Gene Name NO. Arabidopsisthaliana NP_180887.1 504 Ricinus communis XP_002528332.1 505 Glycine maxXP_003530311.1 506 Zea mays DAA60407.1 507 Medicago truncatulaXP_003619209.1 508 Physcomitrella patens XP_001753516.1 509 Sorghumbicolor XP_002459773.1 510 Oryza sativa EAZ03669.1 511 Brachypodiumdistachyon XP_003563196.1 512 Populus trichocarpa XP_002315593.1 513Vitis vinifera XP_002282386.1 514 Cucumis sativus XP_004134031.1 515Arabidopsis lyrata XP_002879445.1 516

In some embodiments, a SUVH2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVH2 protein (SEQ ID NO: 504).

A SUVH2-like protein may include the amino acid sequence or a fragmentthereof of any SUVH2 homolog or ortholog, such as any one of thoselisted in Table 26. One of skill would readily recognize that additionalSUVH2 homologs and/or orthologs may exist and may be used herein.

SUVH9 Proteins

Certain aspects of the present disclosure relate to SUVH9-like proteins.In some embodiments, a SUVH9-like protein refers to a recombinant SUVH9protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a SUVH9-like protein refers to arecombinant SUVH9 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a SUVH9-like proteinrefers to a recombinant SUVH9 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aSUVH9-like protein refers to a recombinant SUVH9 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.SUVH9-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

SUVH9 proteins are known in the art and are described herein. In someembodiments, a SUVH9 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length SUVH9 protein. In some embodiments, SUVH9 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length SUVH9 protein. In someembodiments, SUVH9 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVH9 protein. In someembodiments, SUVH9 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVH9 protein.

Suitable SUVH9 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVH9 proteins may include, for example, thoselisted in Table 27, homologs thereof, and orthologs thereof.

TABLE 27 SUVH9 Proteins SEQ ID Organism Gene Name NO: Arabidopsisthaliana AF344452.1 517 Ricinus communis XP_002528332.1 518 Glycine maxXP_003530311.1 519 Zea mays DAA60407.1 520 Medicago truncatulaXP_003619209.1 521 Physcomitrella patens XP_001753516.1 522 Sorghumbicolor XP_002459773.1 523 Oryza sativa EAZ03669.1 524 Brachypodiumdistachyon XP_003563196.1 525 Populus trichocarpa XP_002315593.1 526Vitis vinifera XP_002282386.1 527 Cucumis sativus XP_004134031.1 528Arabidopsis lyrata XP_002863127.1 529

In some embodiments, a SUVH9 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVH9 protein (SEQ ID NO: 517).

A SUVH9-like protein may include the amino acid sequence or a fragmentthereof of any SUVH9 homolog or ortholog, such as any one of thoselisted in Table 27. One of skill would readily recognize that additionalSUVH9 homologs and/or orthologs may exist and may be used herein.

SUVH2 and SUVH9 proteins of the present disclosure are SU-VAR (3-9)Homologs. Full-length SUVH2 and SUVH9 proteins contain a two-helixbundle domain towards the N-terminus, a SRA domain, and the pre-SET andSET domains towards the C-terminus. The structural and sequence featuresof the SUVH domains are known in the art and are provided herein. Insome embodiments, SUVH2-like proteins and/or SUVH9-like proteins of thepresent disclosure may contain one or more of the canonical SUVH domainsincluding a two-helix bundle domain, a SRA domain, a pre-SET domain,and/or a SET domain.

DMS3 Proteins

Certain aspects of the present disclosure relate to DMS3-like proteins.In some embodiments, a DMS3-like protein refers to a recombinant DMS3protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a DMS3-like protein refers to a recombinantDMS3 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a DMS3-like protein refers to arecombinant DMS3 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a DMS3-likeprotein refers to a recombinant DMS3 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. DMS3-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

DMS3 proteins are known in the art and are described herein. In someembodiments, a DMS3 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DMS3 protein. In some embodiments, DMS3 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DMS3 protein. In someembodiments, DMS3 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DMS3 protein. In someembodiments, DMS3 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DMS3 protein.

Suitable DMS3 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable DMS3 proteins may include, for example, thoselisted in Table 28, homologs thereof, and orthologs thereof.

TABLE 28 DMS3 Proteins SEQ ID Organism Gene Name NO: Arabidopsisthaliana DMS3 531 Solanum lycopersicum XP_004234924.1 532 Solanumtuberosum XP_006350630.1 533 Phaseolus vulgaris ESW19314.1 534 Vitisvinifera XP_002277586.1 535 Theobroma cacao EOY23566.1 536 Glycine maxXP_003550866.1 537 Oriza sativa Japonica group NP_001042520.1 538 Orizasativa Indica group EEC70256.1 539 Zea mays NP_001132336.1 540 Sorghumbicolor XP_002454876.1 541

In some embodiments, a DMS3 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DMS3 protein (SEQ ID NO: 531).

A DMS3-like protein may include the amino acid sequence or a fragmentthereof of any DMS3 homolog or ortholog, such as, for example, any oneof those listed in Table 28. One of skill would readily recognize thatadditional DMS3 homologs and/or orthologs may exist and may be usedherein.

MORC6 Proteins

Certain aspects of the present disclosure relate to MORC6-like proteins.In some embodiments, a MORC6-like protein refers to a recombinant MORC6protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a MORC6-like protein refers to arecombinant MORC6 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a MORC6-like proteinrefers to a recombinant MORC6 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aMORC6-like protein refers to a recombinant MORC6 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.MORC6-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

MORC6 proteins are known in the art and are described herein. In someembodiments, a MORC6 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length MORC6 protein. In some embodiments, MORC6 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length MORC6 protein. In someembodiments, MORC6 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length MORC6 protein. In someembodiments, MORC6 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length MORC6 protein.

Suitable MORC6 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable MORC6 proteins may include, for example, thoselisted in Table 29, homologs thereof, and orthologs thereof.

TABLE 29 MORC6 Proteins SEQ ID Organism Gene Name NO: Arabidopsisthaliana MORC6 542 Solanum lycopersicum XP_004230214.1 543 Solanumtuberosum XP_006344837.1 544 Phaseolus vulgaris ESW10038.1 545 Vitisvinifera XP_002278685.1 546 Theobroma cacao EOY20772.1 547 Triticumurarte EMS64080.1 548 Glycine max XP_003523086.1 549 Oriza sativaJaponica group EEE54777.1 550 Oriza sativa Indica group EEC70857.1 551Zea mays AFW84846.1 552 Sorghum bicolor XP_002455787.1 553

In some embodiments, a MORC6 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana MORC6 protein (SEQ ID NO: 542).

A MORC6-like protein may include the amino acid sequence or a fragmentthereof of any MORC6 homolog or ortholog, such as, for example, any oneof those listed in Table 29. One of skill would readily recognize thatadditional MORC6 homologs and/or orthologs may exist and may be usedherein.

SUVR2 Proteins

Certain aspects of the present disclosure relate to SUVR2-like proteins.In some embodiments, a SUVR2-like protein refers to a recombinant SUVR2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a SUVR2-like protein refers to arecombinant SUVR2 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a SUVR2-like proteinrefers to a recombinant SUVR2 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aSUVR2-like protein refers to a recombinant SUVR2 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.SUVR2-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

SUVR2 proteins are known in the art and are described herein. In someembodiments, a SUVR2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length SUVR2 protein. In some embodiments, SUVR2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length SUVR2 protein. In someembodiments, SUVR2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVR2 protein. In someembodiments, SUVR2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVR2 protein.

Suitable SUVR2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVR2 proteins may include, for example, thoselisted in Table 30, homologs thereof, and orthologs thereof.

TABLE 30 SUVR2 Proteins SEQ ID Organism Gene Name NO: Arabidopsisthaliana SUVR2 554 Solanum lycopersicum XP_004247936.1 555 Solanumtuberosum XP_006358446.1 556 Phaseolus vulgaris ESW16847.1 557 Vitisvinifera XP_002270320.2 558 Theobroma cacao EOX94338.1 559 Triticumurarte EMS67506.1 560 Glycine max XP_003541369.1 561 Oriza sativaJaponica group NP_001047458.1 562 Oriza sativa Indica group EEC78330.1563 Zea mays DAA48520.1 564 Sorghum bicolor XP_002445655.1 565

In some embodiments, a SUVR2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVR2 protein (SEQ ID NO: 554).

A SUVR2-like protein may include the amino acid sequence or a fragmentthereof of any SUVR2 homolog or ortholog, such as, for example, any oneof those listed in Table 30. One of skill would readily recognize thatadditional SUVR2 homologs and/or orthologs may exist and may be usedherein.

DRD1 Proteins

Certain aspects of the present disclosure relate to DRD1-like proteins.In some embodiments, a DRD1-like protein refers to a recombinant DRD1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a DRD1-like protein refers to a recombinantDRD1 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a DRD1-like protein refers to arecombinant DRD1 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a DRD1-likeprotein refers to a recombinant DRD1 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. DRD1-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

DRD1 proteins are known in the art and are described herein. In someembodiments, a DRD1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRD1 protein. In some embodiments, DRD1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRD1 protein. In someembodiments, DRD1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRD1 protein. In someembodiments, DRD1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRD1 protein.

Suitable DRD1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable DRD1 proteins may include, for example, those listed in Table31, homologs thereof, and orthologs thereof.

TABLE 31 DRD1 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_179232.1 566 Ricinus communis XP_002530324.1 567 Glycine maxXP_003540522.1 568 Zea mays AFW57413.1 569 Physcomitrella patensXP_001752976.1 570 Sorghum bicolor XP_002445019.1 571 Oryza sativaBAC84084.1 572 Brachypodium distachyon XP_003571619.1 573 Populustrichocarpa XP_002313774.2 574 Vitis vinifera XP_002273814.1 575 Cucumissativus XP_004170971.1 576 Arabidopsis lyrata XP_002884170.1 577

In some embodiments, a DRD1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRD1 protein (SEQ ID NO: 566).

A DRD1-like protein may include the amino acid sequence or a fragmentthereof of any DRD1 homolog or ortholog, such as, for example, any oneof those listed in Table 31. One of skill would readily recognize thatadditional DRD1 homologs and/or orthologs may exist and may be usedherein.

RDM1 Proteins

Certain aspects of the present disclosure relate to RDM1-like proteins.In some embodiments, a RDM1-like protein refers to a recombinant RDM1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a RDM1-like protein refers to a recombinantRDM1 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a RDM1-like protein refers to arecombinant RDM1 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a RDM1-likeprotein refers to a recombinant RDM1 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. RDM1-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

RDM1 proteins are known in the art and are described herein. In someembodiments, a RDM1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length RDM1 protein. In some embodiments, RDM1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length RDM1 protein. In someembodiments, RDM1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length RDM1 protein. In someembodiments, RDM1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length RDM1 protein.

Suitable RDM1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, and Oryzasativa. Examples of suitable RDM1 proteins may include, for example,those listed in Table 32, homologs thereof, and orthologs thereof.

TABLE 32 RDM1 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_188907.2 578 Ricinus communis XP_002517093.1 579 Glycine maxNP_001237231.1 580 Zea mays NP_001170520.1 581 Medicago truncatulaXP_003610752.1 582 Oryza sativa BAD38576.1 583 Populus trichocarpaXP_002311634.1 584 Vitis vinifera XP_002279112.2 585 Cucumis sativusXP_004134127.1 586 Arabidopsis lyrata XP_002883375.1 587

In some embodiments, a RDM1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana RDM1 protein (SEQ ID NO: 578).

A RDM1-like protein may include the amino acid sequence or a fragmentthereof of any RDM1 homolog or ortholog, such as, for example, any oneof those listed in Table 32. One of skill would readily recognize thatadditional RDM1 homologs and/or orthologs may exist and may be usedherein.

DRM3 Proteins

Certain aspects of the present disclosure relate to DRM3-like proteins.In some embodiments, a DRM3-like protein refers to a recombinant DRM3protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a DRM3-like protein refers to a recombinantDRM3 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a DRM3-like protein refers to arecombinant DRM3 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a DRM3-likeprotein refers to a recombinant DRM3 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. DRM3-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

DRM3 proteins are known in the art and are described herein. In someembodiments, a DRM3 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRM3 protein. In some embodiments, DRM3 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRM3 protein. In someembodiments, DRM3 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRM3 protein. In someembodiments, DRM3 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRM3 protein.

Suitable DRM3 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable DRM3 proteins may include, for example, those listed in Table33, homologs thereof, and orthologs thereof.

TABLE 33 DRM3 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_566573.1 588 Ricinus communis XP_002519294.1 589 Glycine maxXP_006583974.1 590 Zea mays NP_001105094.1 591 Medicago truncatulaXP_003609841.1 592 Sorghum bicolor XP_002468285.1 593 Oryza sativaAAT85176.1 594 Brachypodium distachyon XP_003569077.1 595 Populustrichocarpa XP_002316067.2 596 Vitis vinifera XP_002264226.1 597 Cucumissativus XP_004138523.1 598 Arabidopsis lyrata XP_002885200.1 599

In some embodiments, a DRM3 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRM3 protein (SEQ ID NO: 588).

A DRM3-like protein may include the amino acid sequence or a fragmentthereof of any DRM3 homolog or ortholog, such as, for example, any oneof those listed in Table 33. One of skill would readily recognize thatadditional DRM3 homologs and/or orthologs may exist and may be usedherein.

DRM2 Proteins

Certain aspects of the present disclosure relate to DRM2-like proteins.In some embodiments, a DRM2-like protein refers to a recombinant DRM2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a DRM2-like protein refers to a recombinantDRM2 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a DRM2-like protein refers to arecombinant DRM2 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a DRM2-likeprotein refers to a recombinant DRM2 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. DRM2-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

DRM2 proteins are known in the art and are described herein. In someembodiments, a DRM2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRM2 protein. In some embodiments, DRM2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRM2 protein. In someembodiments, DRM2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRM2 protein. In someembodiments, DRM2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRM2 protein.

Suitable DRM2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Nicotiana tabacum, Ricinus communis, Glycine max, ZeaMays, Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examplesof suitable DRM2 proteins may include, for example, those listed inTable 34, homologs thereof, and orthologs thereof.

TABLE 34 DRM2 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_196966.2 600 Ricinus communis XP_002521449.1 601 Glycine maxXP_003524549.1 602 Zea mays NP_001104977.1 603 Medicago truncatulaXP_003618189.1 604 Sorghum bicolor XP_002468660.1 605 Oryza salivaABF93591.1 606 Brachypodium distachyon XP_003575456.1 607 Populustrichocarpa XP_002300046.2 608 Vitis vinifera XP_002273972.2 609 Cucumissativus XP_004141100.1 610 Arabidopsis lyrata XP_002873681.1 611Nicotiana tabacum NP_001313186.1 678

In some embodiments, a DRM2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRM2 protein (SEQ ID NO: 600), or to SEQ ID NO: 678.

A DRM2-like protein may include the amino acid sequence or a fragmentthereof of any DRM2 homolog or ortholog, such as, for example, any oneof those listed in Table 34. One of skill would readily recognize thatadditional DRM2 homologs and/or orthologs may exist and may be usedherein.

In some embodiments, the fragment of DRM2 is a fragment that containsthe catalytic (methyltransferase) domain of DRM2. In some embodiments,the fragment is a DRM2-MTase fragment from tobacco (e.g. SEQ ID NO:679), or a homolog or ortholog thereof. In some embodiments, aDRM2-MTase fragment of the present disclosure has an amino acid sequencewith at least about 20%, at least about 25%, at least about 30%, atleast about 40%, at least about 50%, at least about 55%, at least about60%, at least about 65%, at least about 70%, at least about 75%, atleast about 80%, at least about 85%, at least about 90%, at least about91%, at least about 92%, at least about 93%, at least about 94%, atleast about 95%, at least about 96%, at least about 97%, at least about98%, at least about 99%, or at least about 100% amino acid identity tothe amino acid sequence of SEQ ID NO: 679.

FRG Proteins

Certain aspects of the present disclosure relate to FRG-like proteins.In some embodiments, a FRG-like protein refers to a recombinant FRGprotein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a FRG-like protein refers to a recombinantFRG protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a FRG-like protein refers to arecombinant FRG protein or fragment thereof that is fused to an MS2 coatprotein or fragment thereof. In some embodiments, a FRG-like proteinrefers to a recombinant FRG protein or fragment thereof that is fused toan scFV antibody or fragment thereof. FRG-like proteins may be used inreducing the expression of one or more target nucleic acids, such asgenes, in plants.

FRG proteins are known in the art and are described herein. In someembodiments, a FRG protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length FRG protein. In some embodiments, FRG protein fragments mayinclude sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length FRG protein. In someembodiments, FRG protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length FRG protein. In someembodiments, FRG protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length FRG protein.

Suitable FRG proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable FRG proteins may include, for example, those listed in Table35, homologs thereof, and orthologs thereof.

TABLE 35 FRG Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaNP_188635.1 612 Ricinus communis XP_002513133.1 613 Glycine maxXP_003555190.1 614 Zea mays AFW61101.1 615 Medicago truncatulaXP_003593498.1 616 Physcomitrella patens XP_001770987.1 617 Sorghumbicolor XP_002458594.1 618 Oryza sativa NP_001061138.1 619 Brachypodiumdistachyon XP_003560909.1 620 Populus trichocarpa XP_002305010.2 621Vitis vinifera XP_002267403 622 Cucumis sativus XP_004134959 623Arabidopsis lyrata XP_002883222.1 624

In some embodiments, a FRG protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana FRG protein (SEQ ID NO: 612).

A FRG-like protein may include the amino acid sequence or a fragmentthereof of any FRG homolog or ortholog, such as, for example, any one ofthose listed in Table 35. One of skill would readily recognize thatadditional FRG homologs and/or orthologs may exist and may be usedherein.

ATRX Proteins

Certain aspects of the present disclosure relate to ATRX-like proteins.In some embodiments, an ATRX-like protein refers to a recombinant ATRXprotein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, an ATRX-like protein refers to arecombinant ATRX protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, an ATRX-like proteinrefers to a recombinant ATRX protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, anATRX-like protein refers to a recombinant ATRX protein or fragmentthereof that is fused to an scFV antibody or fragment thereof. ATRX-likeproteins may be used in reducing the expression of one or more targetnucleic acids, such as genes, in plants.

ATRX proteins are known in the art and are described herein. In someembodiments, an ATRX protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length ATRX protein. In some embodiments, ATRX protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length ATRX protein. In someembodiments, ATRX protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length ATRX protein. In someembodiments, ATRX protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length ATRX protein.

Suitable ATRX proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Sorghumbicolor, and Oryza sativa. Examples of suitable ATRX proteins mayinclude, for example, those listed in Table 36, homologs thereof, andorthologs thereof.

TABLE 36 ATRX Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_001184937 681 Arabidopsis lyrata XP_002889705 682 Cucumissativus XP_011649017.1 683 Vitis vinifera XP_010660172.1 684 Medicagotruncatula XP_003590986.2 685 Ricinus communis EEF40405.1 686 Glycinemax XP_014618708.1 687 Zea mays NP_001295442.1 688 Sorghum bicolorKXG38419.1 689 Oryza sativa XP_015614509.1 690 Brachypodium distachyonXP_003571839.1 691 Populus trichocarpa XP_002319663.2 692 Brassica napusCDX95047.1 693

In some embodiments, a ATRX protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana ATRX protein (SEQ ID NO: 681).

An ATRX-like protein may include the amino acid sequence or a fragmentthereof of any ATRX homolog or ortholog, such as, for example, any oneof those listed in Table 36. One of skill would readily recognize thatadditional ATRX homologs and/or orthologs may exist and may be usedherein.

MOM1 Proteins

Certain aspects of the present disclosure relate to MOM1-like proteins.In some embodiments, a MOM1-like protein refers to a recombinant MOM1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a MOM1-like protein refers to a recombinantMOM1 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a MOM1-like protein refers to arecombinant MOM1 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a MOM1-likeprotein refers to a recombinant MOM1 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. MOM1-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

MOM1 proteins are known in the art and are described herein. In someembodiments, an MOM1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length MOM1 protein. In some embodiments, MOM1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length MOM1 protein. In someembodiments, MOM1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length MOM1 protein. In someembodiments, MOM1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length MOM1 protein.

Suitable MOM1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Sorghumbicolor, and Oryza sativa. Examples of suitable MOM1 proteins mayinclude, for example, those listed in Table 37, homologs thereof, andorthologs thereof.

TABLE 37 MOM1 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_563806.1 694 Arabidopsis lyrata XP_002892431.1 695 Cucumissativus XP_011653950.1 696 Vitis vinifera XP_010651197.1 697 Medicagotruncatula XP_013465325.1 698 Ricinus communis EEF32941.1 699 Glycinemax KRH26470.1 700 Zea mays XP_008659422.1 701 Sorghum bicolor KXG19083702 Oryza sativa BAS95710.1 703 Brachypodium distachyon KQJ86790 704Populus trichocarpa XP_002318937.1 705 Brassica napus XP_013711471 706

In some embodiments, a MOM1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana MOM1 protein (SEQ ID NO: 694).

A MOM1-like protein may include the amino acid sequence or a fragmentthereof of any MOM1 homolog or ortholog, such as, for example, any oneof those listed in Table 37. One of skill would readily recognize thatadditional MOM1 homologs and/or orthologs may exist and may be usedherein.

MORC1 Proteins

Certain aspects of the present disclosure relate to MORC1-like proteins.In some embodiments, a MORC1-like protein refers to a recombinant MORC1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a MORC1-like protein refers to arecombinant MORC1 protein or fragment thereof that is fused to a CAS9protein or fragment thereof. In some embodiments, a MORC1-like proteinrefers to a recombinant MORC1 protein or fragment thereof that is fusedto an MS2 coat protein or fragment thereof. In some embodiments, aMORC1-like protein refers to a recombinant MORC1 protein or fragmentthereof that is fused to an scFV antibody or fragment thereof.MORC1-like proteins may be used in reducing the expression of one ormore target nucleic acids, such as genes, in plants.

MORC1 proteins are known in the art and are described herein. In plants,MORC1 was first identified to be involved in plant disease resistancesignaling (Kang H G et al, 208a, 2008b, 2010). More recently, MORC1 hasbeen shown to be involved in gene silencing and chromatin compaction,although the mechanism of action is not well understood (Moissard, G etal, 2012, 2014, Liu Z W et al, 2014).

In some embodiments, an MORC1 protein fragment contains at least 20consecutive amino acids, at least 30 consecutive amino acids, at least40 consecutive amino acids, at least 50 consecutive amino acids, atleast 60 consecutive amino acids, at least 70 consecutive amino acids,at least 80 consecutive amino acids, at least 90 consecutive aminoacids, at least 100 consecutive amino acids, at least 120 consecutiveamino acids, at least 140 consecutive amino acids, at least 160consecutive amino acids, at least 180 consecutive amino acids, at least200 consecutive amino acids, at least 220 consecutive amino acids, atleast 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length MORC1 protein. In some embodiments, MORC1 proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length MORC1 protein.In some embodiments, MORC1 protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-length MORC1protein. In some embodiments, MORC1 protein fragments may includesequences with one or more amino acids added to an otherwise consecutiveamino acid sequence of a full-length MORC1 protein.

Suitable MORC1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Sorghumbicolor, and Oryza sativa. Examples of suitable MORC1 proteins mayinclude, for example, those listed in Table 38, homologs thereof, andorthologs thereof.

TABLE 38 MORC1 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_568000.1 707 Arabidopsis lyrata XP_002867022.1 708 Cucumissativus XP_011653148.1 709 Vitis vinifera XP_002267687.2 710 Medicagotruncatula XP_013446369.1 711 Ricinus communis XP_002533659.2 712Glycine max KRH69835.1 713 Zea mays XP_008675511.1 714 Sorghum bicolorKXG24418.1 715 Oryza sativa AAK70637.1 716 Brachypodium distachyonXP_003573822.1 717 Populus trichocarpa XP_006383149.1 718 Brassica napusXP_013745728.1 719

In some embodiments, a MORC1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana MORC1 protein (SEQ ID NO: 707).

A MORC1-like protein may include the amino acid sequence or a fragmentthereof of any MORC1 homolog or ortholog, such as, for example, any oneof those listed in Table 38. One of skill would readily recognize thatadditional MORC1 homologs and/or orthologs may exist and may be usedherein.

SssI Proteins

Certain aspects of the present disclosure relate to SssI-like proteins.In some embodiments, a SssI-like protein refers to a recombinant SssIprotein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a SssI-like protein refers to a recombinantSssI protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a SssI-like protein refers to arecombinant SssI protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a SssI-likeprotein refers to a recombinant SssI protein or fragment thereof that isfused to an scFV antibody or fragment thereof. SssI-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

SssI proteins are known in the art and are described herein. SssI is aDNA methyltransferase from the bacteria Spiroplasma sp. with homologs inother bacterial species.

In some embodiments, an SssI protein fragment contains at least 20consecutive amino acids, at least 30 consecutive amino acids, at least40 consecutive amino acids, at least 50 consecutive amino acids, atleast 60 consecutive amino acids, at least 70 consecutive amino acids,at least 80 consecutive amino acids, at least 90 consecutive aminoacids, at least 100 consecutive amino acids, at least 120 consecutiveamino acids, at least 140 consecutive amino acids, at least 160consecutive amino acids, at least 180 consecutive amino acids, at least200 consecutive amino acids, at least 220 consecutive amino acids, atleast 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length SssI protein. In some embodiments, SssI proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length SssI protein.In some embodiments, SssI protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-length SssIprotein. In some embodiments, SssI protein fragments may includesequences with one or more amino acids added to an otherwise consecutiveamino acid sequence of a full-length SssI protein.

Suitable SssI proteins may be identified and isolated from suitablebacterial species. Examples of suitable SssI proteins may include, forexample, those listed in Table 39, homologs thereof, and orthologsthereof.

TABLE 39 SssI Proteins Organism Gene Name SEQ ID NO: Spiroplasmamonobiae P15840.3 680 Mycoplasma penetrans WP_011077318.1 748Acholeplasma sp. CAG: 878 CCY28146.1 749 Mycoplasma hyosynoviaeKDE43677.1 750 Mesoplasma seiffertii WP_051418436.1 751 Clostridiumdiolis WP_039773024.1 752 Streptococcus sanguinis WP_011837382.1 753

In some embodiments, a SssI protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the SssIprotein (SEQ ID NO: 680).

A SssI-like protein may include the amino acid sequence or a fragmentthereof of any SssI homolog or ortholog, such as, for example, any oneof those listed in Table 39. One of skill would readily recognize thatadditional SssI homologs and/or orthologs may exist and may be usedherein.

In some aspects, use of an SssI-like protein according to the methods ofthe present disclosure may result in genome-wide methylation of nucleicacids as compared to a corresponding control.

Other bacterial CpG methyltransferase enzymes may also be used in themethods and compositions of the present disclosure. Exemplary bacterialCpG methyltransferases include M.MpeI proteins, such as M.MpeI fromMycoplasma penetrans HF-2 (SEQ ID NO: 754).

Various other bacterial DNA cytosine methyltransferases may also be usedin the methods and compositions of the present disclosure. Exemplarybacterial DNA cytosine methyltransferases include HhaI proteins, such asHhaI from Haemophilus parahaemolyticus (SEQ ID NO: 755). HhaI is a GCGCspecific methylase.

DNMT3A Proteins

Certain aspects of the present disclosure relate to DNMT3A-likeproteins. In some embodiments, a DNMT3A-like protein refers to arecombinant DNMT3A protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, a DNMT3A-likeprotein refers to a recombinant DNMT3A protein or fragment thereof thatis fused to a CAS9 protein or fragment thereof. In some embodiments, aDNMT3A-like protein refers to a recombinant DNMT3A protein or fragmentthereof that is fused to an MS2 coat protein or fragment thereof. Insome embodiments, a DNMT3A-like protein refers to a recombinant DNMT3Aprotein or fragment thereof that is fused to an scFV antibody orfragment thereof. DNMT3A-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

DNMT3A proteins are known in the art and are described herein. In someembodiments, an DNMT3A protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DNMT13A protein. In some embodiments, DNMT3A proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length DNMT3Aprotein. In some embodiments, DNMT3A protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length DNMT3A protein. In some embodiments, DNMT3A proteinfragments may include sequences with one or more amino acids added to anotherwise consecutive amino acid sequence of a full-length DNMT3Aprotein.

Suitable DNMT3A proteins may be identified and isolated from variousspecies Examples of suitable DNMT3A proteins may include, for example,those listed in Table 40, homologs thereof, and orthologs thereof.

TABLE 40 DNMT3A Proteins Organism Gene Name SEQ ID NO: Mus musculusNP_031898.1 861 Homo sapiens NP_072046.2 808 Pan Paniscus XP_008950657809 Rattus norvegicus NP_001003958.1 810 Rhinolophus sinicusXP_019568274.1 811 Equus caballus XP_005600228.1 812 Ovis ariesXP012021398.1 813 Bos Taurus AAP75901.1 814 Orcinus orca XP_012387866.1815 Ictidomys tridecemlineatus XP_005322636.1 816 Monodelphis domesticaXP_016286174.1 817

In some embodiments, a DNMT3A protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the Musmusculus DNMT3A protein (SEQ ID NO: 861).

A DNMT3A-like protein may include the amino acid sequence or a fragmentthereof of any DNMT3A homolog or ortholog, such as, for example, any oneof those listed in Table 40. One of skill would readily recognize thatadditional DNMT3A homologs and/or orthologs may exist and may be usedherein.

In some embodiments, the catalytic domain of a DNMT3A protein (e.g. SEQID NO: 818) may be used in a polypeptide of the present disclosure. Insome embodiments, a DNMT3A polypeptide of the present disclosure has anamino acid sequence with at least about 20%, at least about 25%, atleast about 30%, at least about 40%, at least about 50%, at least about55%, at least about 60%, at least about 65%, at least about 70%, atleast about 75%, at least about 80%, at least about 85%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, or at least about 100%amino acid identity to the amino acid sequence of SEQ ID NO: 818.

DNMT3L Proteins

Certain aspects of the present disclosure relate to DNMT3L-likeproteins. In some embodiments, a DNMT3L-like protein refers to arecombinant DNMT3L protein or fragment thereof and that contains aheterologous DNA-binding domain. In some embodiments, a DNMT3L-likeprotein refers to a recombinant DNMT3L protein or fragment thereof thatis fused to a CAS9 protein or fragment thereof. In some embodiments, aDNMT3L-like protein refers to a recombinant DNMT3L protein or fragmentthereof that is fused to an MS2 coat protein or fragment thereof. Insome embodiments, a DNMT3L-like protein refers to a recombinant DNMT3Lprotein or fragment thereof that is fused to an scFV antibody orfragment thereof. DNMT3L-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

DNMT3L proteins are known in the art and are described herein. In someembodiments, an DNMT3L protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DNMT3L protein. In some embodiments, DNMT3L proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length DNMT3Lprotein. In some embodiments, DNMT3L protein fragments may includesequences with one or more amino acids replaced/substituted with anamino acid different from the endogenous amino acid present at a givenamino acid position in a consecutive amino acid sequence of afull-length DNMT3L protein. In some embodiments, DNMT3L proteinfragments may include sequences with one or more amino acids added to anotherwise consecutive amino acid sequence of a full-length DNMT3Lprotein.

Suitable DNMT3L proteins may be identified and isolated from variousspecies Examples of suitable DNMT3L proteins may include, for example,those listed in Table 41, homologs thereof, and orthologs thereof.

TABLE 41 DN1VIT3L Proteins Organism Gene Name SEQ ID NO: Mus musculusNP_062321.1 819 Pan paniscus XP_003823892.1 820 Rattus norvegicusNP_00103964.1 821 Rhinolophus sinicus XP_019601251.1 822 Equus caballusXP_014591962.1 823 Ovis aries XP_014947250.1 824 Bos TaurusXP_010822784.1 825 Orcinus orca XP_004264713.1 826 Ictidomystridecemlineatus XP_005323631.1 827 Monodelphis domestica XP_007493361.1828 Homo sapiens NP_037501.2 862

In some embodiments, a DNMT3L protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the Musmusculus DNMT3L protein (SEQ ID NO: 819).

A DNMT3L-like protein may include the amino acid sequence or a fragmentthereof of any DNMT3L homolog or ortholog, such as, for example, any oneof those listed in Table 41. One of skill would readily recognize thatadditional DNMT3L homologs and/or orthologs may exist and may be usedherein.

In some embodiments, the C-terminal region of a DNMT3L protein (e.g. SEQID NO: 829) may be used in a polypeptide of the present disclosure. Insome embodiments, a DNMT3L polypeptide of the present disclosure has anamino acid sequence with at least about 20%, at least about 25%, atleast about 30%, at least about 40%, at least about 50%, at least about55%, at least about 60%, at least about 65%, at least about 70%, atleast about 75%, at least about 80%, at least about 85%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, or at least about 100%amino acid identity to the amino acid sequence of SEQ ID NO: 829.

In some embodiments, fusion proteins containing DNMT3A amino acidsequences fused with DNMT3L amino acid sequences may be used. In someembodiments, a DNMT3A-DNMT3L fusion protein of the present disclosurehas an amino acid sequence with at least about 20%, at least about 25%,at least about 30%, at least about 40%, at least about 50%, at leastabout 55%, at least about 60%, at least about 65%, at least about 70%,at least about 75%, at least about 80%, at least about 85%, at leastabout 90%, at least about 91%, at least about 92%, at least about 93%,at least about 94%, at least about 95%, at least about 96%, at leastabout 97%, at least about 98%, at least about 99%, or at least about100% amino acid identity to the amino acid sequence of SEQ ID NO: 859.

MBD9 Proteins

Certain aspects of the present disclosure relate to MBD9-like proteins.In some embodiments, a MBD9-like protein refers to a recombinant MBD9protein or fragment thereof and that contains a heterologous DNA-bindingdomain. In some embodiments, a MBD9-like protein refers to a recombinantMBD9 protein or fragment thereof that is fused to a CAS9 protein orfragment thereof. In some embodiments, a MBD9-like protein refers to arecombinant MBD9 protein or fragment thereof that is fused to an MS2coat protein or fragment thereof. In some embodiments, a MBD9-likeprotein refers to a recombinant MBD9 protein or fragment thereof that isfused to an scFV antibody or fragment thereof. MBD9-like proteins may beused in reducing the expression of one or more target nucleic acids,such as genes, in plants.

MBD9 proteins are known in the art and are described herein. FIG. 41provides an alignment of all MBD proteins in Arabidopsis plus three fromhumans, and illustrates high conservation of key residues in themethyl-binding domain.

In some embodiments, an MBD9 protein fragment contains at least 20consecutive amino acids, at least 30 consecutive amino acids, at least40 consecutive amino acids, at least 50 consecutive amino acids, atleast 60 consecutive amino acids, at least 70 consecutive amino acids,at least 80 consecutive amino acids, at least 90 consecutive aminoacids, at least 100 consecutive amino acids, at least 120 consecutiveamino acids, at least 140 consecutive amino acids, at least 160consecutive amino acids, at least 180 consecutive amino acids, at least200 consecutive amino acids, at least 220 consecutive amino acids, atleast 240 consecutive amino acids, or 241 or more consecutive aminoacids of a full-length MBD9 protein. In some embodiments, MBD9 proteinfragments may include sequences with one or more amino acids removedfrom the consecutive amino acid sequence of a full-length MBD9 protein.In some embodiments, MBD9 protein fragments may include sequences withone or more amino acids replaced/substituted with an amino aciddifferent from the endogenous amino acid present at a given amino acidposition in a consecutive amino acid sequence of a full-length MBD9protein. In some embodiments, MBD9 protein fragments may includesequences with one or more amino acids added to an otherwise consecutiveamino acid sequence of a full-length MBD9 protein.

Suitable MBD9 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Sorghumbicolor, and Oryza sativa. Examples of suitable MBD9 proteins mayinclude, for example, those listed in Table 42, homologs thereof, andorthologs thereof.

TABLE 42 MBD9 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_186795.1 830 Arabidopsis lyrata XP_002884279.1 831 Cucumissativus KGN59651.1 832 Vitis vinifera XP_010660927.1 833 Medicagotruncatula XP_013450825.1 834 Ricinus communis XP_015573615.1 835Glycine max XP_006594288.1 836 Zea mays AQK60154.1 837 Sorghum bicolorKXG29684.1 838 Oryza sativa EEE56485.1 839 Brachypodium distachyonXP_003571114.3 840 Populus trichocarpa XP_002324010.2 841 Brassica napusCDY28674.1 842

In some embodiments, a MBD9 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana MBD9 protein (SEQ ID NO: 830).

A MBD9-like protein may include the amino acid sequence or a fragmentthereof of any MBD9 homolog or ortholog, such as, for example, any oneof those listed in Table 42. One of skill would readily recognize thatadditional MBD9 homologs and/or orthologs may exist and may be usedherein.

Other Epigenetic Regulators

Various other epigenetic regulators may be used according to the methodsof the present disclosure to target and silence a specific nucleic acid.Other exemplary proteins include DCL3 and SPT5L. DCL3 encodes aribonuclease III family protein. An exemplary DCL3 protein includes,using A. thaliana as an exemplary host plant, SEQ ID NO: 391. SPT5L is amember of the nuclear SPT5 (Suppressor of Ty insertion 5) RNA polymerase(RNAP) elongation factor family. An exemplary SPT5L protein includes,using A. thaliana as an exemplary host plant, SEQ ID NO: 392. Theseproteins, as well as homologs and orthologs thereof, may also be used inthe methods and compositions of the present disclosure to target andsilence a specific nucleic acid as described herein for any otherepigenetic regulator-like protein (e.g. AGO4-like proteins).

Other exemplary epigenetic regulators that may be used according to themethods of the present disclosure to target and silence a specificnucleic acid include, for example, DMS4, HEN1, SWI3B, DRB3 and otherHYL1 homologs, DRH1 (At3g01540), DRH2 (At5g14610), UBP26, LDL1, LDL2,RDM16, SR45, STA1, KYP, MET1, VIM1 and other VIM homologs, STRS1, STRS2,ATRX, CHR25, CHR8, MOM1, MOM2 (At2g28240), STP4-1 (At5g08565), SPT4-2(At5g63760), NRPE1, CMT3, CLSY1, IDN2, RDR6, DDM1, HDA8 and homologs andorthologs thereof.

Further, the bacterial CG specific methylase protein, SssI (SEQ ID NO:680), may also be used in the methods and compositions of the presentdisclosure, as well as homologs and orthologs thereof. The mammalian CpGmethyltransferase, DNMT3A, as well as fragments and homologs thereof,may also be used herein. For example, the catalytic domain of a DNMT3Apolypeptide may be used herein (e.g. SEQ ID NO: 807). DNMT3L, as well asfragments and homologs thereof, may also be used herein. In someembodiments, polypeptide fusions of DNMT3A and DNMT3L amino acidsequences may also be used. Exemplary fusions of DNMT3A-DNMT3L maycontain the catalytic domain of a DNMT3A protein, and the C-terminalregion of a DNMT3L protein. An exemplary such fusion is presented in SEQID NO: 859.

Recombinant Nucleic Acids Encoding Recombinant Proteins

Certain aspects of the present disclosure relate to recombinant nucleicacids encoding recombinant proteins of the present disclosure. In someembodiments, recombinant proteins of the present disclosure arerecombinantly fused to a heterologous DNA-binding domain. In someembodiments, recombinant proteins of the present disclosure arerecombinantly fused to a CAS9 protein. In some embodiments, recombinantproteins of the present disclosure are recombinantly fused to an MS2coat protein. In some embodiments, recombinant proteins of the presentdisclosure are recombinantly fused to an scFV antibody. The recombinantproteins may be e.g. SHH1-like proteins, SHH2-like proteins, AGO4-likeproteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-like proteins,JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins.

As used herein, the terms “polynucleotide,” “nucleic acid,” andvariations thereof shall be generic to polydeoxyribonucleotides(containing 2-deoxy-D-ribose), to polyribonucleotides (containingD-ribose), to any other type of polynucleotide that is an N-glycoside ofa purine or pyrimidine base, and to other polymers containingnon-nucleotide backbones, provided that the polymers contain nucleobasesin a configuration that allows for base pairing and base stacking, asfound in DNA and RNA. Thus, these terms include known types of nucleicacid sequence modifications, for example, substitution of one or more ofthe naturally occurring nucleotides with an analog, and inter-nucleotidemodifications. As used herein, the symbols for nucleotides andpolynucleotides are those recommended by the IUPAC-IUB Commission ofBiochemical Nomenclature.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SHH1-like protein. In some embodiments, the recombinantnucleic acid encodes an SHH1 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 1.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SHH2-like protein. In some embodiments, the recombinantnucleic acid encodes an SHH2 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 14.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an AGO4-like protein. In some embodiments, the recombinantnucleic acid encodes an AGO4 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 15.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an HDA6-like protein. In some embodiments, the recombinantnucleic acid encodes an HDA6 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 28.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPD1-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPD1 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 41.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPE1-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPE1 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 54.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a JMJ14-like protein. In some embodiments, the recombinantnucleic acid encodes a JMJ14 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 80.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an RDR2-like protein. In some embodiments, the recombinantnucleic acid encodes an RDR2 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 132.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPD2A/NRPE2-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPD2A/NRPE2 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 145.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB3/NRPD3/NRPE3A-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB3/NRPD3/NRPE3A polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 158.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPE3B-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPE3B polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 171.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB11/NRPD11/NRPE11-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB11/NRPD11/NRPE11 polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 184.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB10/NRPD10/NRPE10-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB10/NRPD10/NRPE10 polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 197.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB12/NRPD12/NRPE12-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB12/NRPD12/NRPE12 polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 209.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB6A/NRPD6A/NRPE6A-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB6A/NRPD6A/NRPE6A polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 221.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB6B/NRPD6B/NRPE6B-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB6B/NRPD6B/NRPE6B polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 234.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB8A/NRPE8A-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPB8A/NRPE8A polypeptide orfragment thereof that has an amino acid sequence that is at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% identical to SEQ ID NO: 247.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB8B/NRPD8B/NRPE8B-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB8B/NRPD8B/NRPE8B polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 260.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPE5-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPE5 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 273.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPD4/NRPE4-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPD4/NRPE4 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 286.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPE7-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPE7 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 299.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPD7-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPD7 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 312.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB5/NRPD5-like protein. In some embodiments, therecombinant nucleic acid encodes an NRPB5/NRPD5 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 325.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB9A/NRPD9A/NRPE9A-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB9A/NRPD9A/NRPE9A polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 337.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an NRPB9B/NRPD9B/NRPE9B-like protein. In some embodiments,the recombinant nucleic acid encodes an NRPB9B/NRPD9B/NRPE9B polypeptideor fragment thereof that has an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 350.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SUVH2-like protein. In some embodiments, therecombinant nucleic acid encodes an SUVH2 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 504.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SUVH9-like protein. In some embodiments, therecombinant nucleic acid encodes an SUVH9 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 517.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an DMS3-like protein. In some embodiments, the recombinantnucleic acid encodes an DMS3 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 531.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an MORC6-like protein. In some embodiments, therecombinant nucleic acid encodes an MORC6 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 542.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SUVR2-like protein. In some embodiments, therecombinant nucleic acid encodes an SUVR2 polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 554.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an DRD1-like protein. In some embodiments, the recombinantnucleic acid encodes an DRD1 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 566.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an RDM1-like protein. In some embodiments, the recombinantnucleic acid encodes an RDM1 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 578.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an DRM3-like protein. In some embodiments, the recombinantnucleic acid encodes an DRM3 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 588.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an DRM2-like protein. In some embodiments, the recombinantnucleic acid encodes an DRM2 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 600.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an FRG-like protein. In some embodiments, the recombinantnucleic acid encodes an FRG polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 612.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an DRM2-MTase-like protein. In some embodiments, therecombinant nucleic acid encodes an DRM2-MTase polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 679.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SssI-like protein. In some embodiments, the recombinantnucleic acid encodes an SssI polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 680.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an ATRX-like protein. In some embodiments, the recombinantnucleic acid encodes an ATRX polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 681.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a MOM1-like protein. In some embodiments, the recombinantnucleic acid encodes a MOM1 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 694.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a MORC1-like protein. In some embodiments, the recombinantnucleic acid encodes a MORC1 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 707.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DNMT3A-like protein. In some embodiments, therecombinant nucleic acid encodes a DNMT3A polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 818.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DNMT3L-like protein. In some embodiments, therecombinant nucleic acid encodes a DNMT3L polypeptide or fragmentthereof that has an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% identical to SEQ ID NO: 829.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DNMT3A-DNMT3L fusion protein. In some embodiments, therecombinant nucleic acid encodes a DNMT3A-DNMT3L fusion polypeptide orfragment thereof that has an amino acid sequence that is at least 50%,at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% identical to SEQ ID NO: 859.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a MBD9-like protein. In some embodiments, the recombinantnucleic acid encodes a MBD9 polypeptide or fragment thereof that has anamino acid sequence that is at least 50%, at least 55%, at least 60%, atleast 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to SEQ ID NO: 830.

Sequences of the polynucleotides of the present disclosure may beprepared by various suitable methods known in the art, including, forexample, direct chemical synthesis or cloning. For direct chemicalsynthesis, formation of a polymer of nucleic acids typically involvessequential addition of 3′-blocked and 5′-blocked nucleotide monomers tothe terminal 5′-hydroxyl group of a growing nucleotide chain, whereineach addition is effected by nucleophilic attack of the terminal5′-hydroxyl group of the growing chain on the 3′-position of the addedmonomer, which is typically a phosphorus derivative, such as aphosphotriester, phosphoramidite, or the like. Such methodology is knownto those of ordinary skill in the art and is described in the pertinenttexts and literature (e.g., in Matteucci et al., (1980) Tetrahedron Lett21:719-722; U.S. Pat. Nos. 4,500,707; 5,436,327; and 5,700,637). Inaddition, the desired sequences may be isolated from natural sources bysplitting DNA using appropriate restriction enzymes, separating thefragments using gel electrophoresis, and thereafter, recovering thedesired polynucleotide sequence from the gel via techniques known tothose of ordinary skill in the art, such as utilization of polymerasechain reactions (PCR; e.g., U.S. Pat. No. 4,683,195).

The nucleic acids employed in the methods and compositions describedherein may be codon optimized relative to a parental template forexpression in a particular host cell. Cells differ in their usage ofparticular codons, and codon bias corresponds to relative abundance ofparticular tRNAs in a given cell type. By altering codons in a sequenceso that they are tailored to match with the relative abundance ofcorresponding tRNAs, it is possible to increase expression of a product(e.g. a polypeptide) from a nucleic acid. Similarly, it is possible todecrease expression by deliberately choosing codons corresponding torare tRNAs. Thus, codon optimization/deoptimization can provide controlover nucleic acid expression in a particular cell type (e.g. bacterialcell, plant cell, mammalian cell, etc.). Methods of codon optimizing anucleic acid for tailored expression in a particular cell type arewell-known to those of skill in the art.

Methods of Identifying Sequence Similarity

Various methods are known to those of skill in the art for identifyingsimilar (e.g. homologs, orthologs, paralogs, etc.) polypeptide and/orpolynucleotide sequences, including phylogenetic methods, sequencesimilarity analysis, and hybridization methods.

Phylogenetic trees may be created for a gene family by using a programsuch as CLUSTAL (Thompson et al. Nucleic Acids Res. 22: 4673-4680(1994); Higgins et al. Methods Enzymol 266: 383-402 (1996)) or MEGA(Tamura et al. Mol. Biol. & Evo. 24:1596-1599 (2007)). Once an initialtree for genes from one species is created, potential orthologoussequences can be placed in the phylogenetic tree and their relationshipsto genes from the species of interest can be determined. Evolutionaryrelationships may also be inferred using the Neighbor-Joining method(Saitou and Nei, Mol. Biol. & Evo. 4:406-425 (1987)). Homologoussequences may also be identified by a reciprocal BLAST strategy.Evolutionary distances may be computed using the Poisson correctionmethod (Zuckerkandl and Pauling, pp. 97-166 in Evolving Genes andProteins, edited by V. Bryson and H. J. Vogel. Academic Press, New York(1965)).

In addition, evolutionary information may be used to predict genefunction. Functional predictions of genes can be greatly improved byfocusing on how genes became similar in sequence (i.e. by evolutionaryprocesses) rather than on the sequence similarity itself (Eisen, GenomeRes. 8: 163-167 (1998)). Many specific examples exist in which genefunction has been shown to correlate well with gene phylogeny (Eisen,Genome Res. 8: 163-167 (1998)). By using a phylogenetic analysis, oneskilled in the art would recognize that the ability to deduce similarfunctions conferred by closely-related polypeptides is predictable.

When a group of related sequences are analyzed using a phylogeneticprogram such as CLUSTAL, closely related sequences typically clustertogether or in the same clade (a group of similar genes). Groups ofsimilar genes can also be identified with pair-wise BLAST analysis (Fengand Doolittle, J. Mol. Evol. 25: 351-360 (1987)). Analysis of groups ofsimilar genes with similar function that fall within one clade can yieldsub-sequences that are particular to the clade. These sub-sequences,known as consensus sequences, can not only be used to define thesequences within each clade, but define the functions of these genes;genes within a clade may contain paralogous sequences, or orthologoussequences that share the same function (see also, for example, Mount,Bioinformatics: Sequence and Genome Analysis Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., page 543 (2001)).

To find sequences that are homologous to a reference sequence, BLASTnucleotide searches can be performed with the BLASTN program, score=100,wordlength=12, to obtain nucleotide sequences homologous to a nucleotidesequence encoding a protein of the disclosure. BLAST protein searchescan be performed with the BLASTX program, score=50, wordlength=3, toobtain amino acid sequences homologous to a protein or polypeptide ofthe disclosure. To obtain gapped alignments for comparison purposes,Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul etal. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-BLAST (inBLAST 2.0) can be used to perform an iterated search that detectsdistant relationships between molecules. See Altschul et al. (1997)supra. When utilizing BLAST, Gapped BLAST, or PSI-BLAST, the defaultparameters of the respective programs (e.g., BLASTN for nucleotidesequences, BLASTX for proteins) can be used.

Methods for the alignment of sequences and for the analysis ofsimilarity and identity of polypeptide and polynucleotide sequences arewell-known in the art.

As used herein “sequence identity” refers to the percentage of residuesthat are identical in the same positions in the sequences beinganalyzed. As used herein “sequence similarity” refers to the percentageof residues that have similar biophysical/biochemical characteristics inthe same positions (e.g. charge, size, hydrophobicity) in the sequencesbeing analyzed.

Methods of alignment of sequences for comparison are well-known in theart, including manual alignment and computer assisted sequence alignmentand analysis. This latter approach is a preferred approach in thepresent disclosure, due to the increased throughput afforded by computerassisted methods. As noted below, a variety of computer programs forperforming sequence alignment are available, or can be produced by oneof skill.

The determination of percent sequence identity and/or similarity betweenany two sequences can be accomplished using a mathematical algorithm.Examples of such mathematical algorithms are the algorithm of Myers andMiller, CABIOS 4:11-17 (1988); the local homology algorithm of Smith etal., Adv. Appl. Math. 2:482 (1981); the homology alignment algorithm ofNeedleman and Wunsch, J. Mol. Biol. 48:443-453 (1970); thesearch-for-similarity-method of Pearson and Lipman, Proc. Natl. Acad.Sci. 85:2444-2448 (1988); the algorithm of Karlin and Altschul, Proc.Natl. Acad. Sci. USA 87:2264-2268 (1990), modified as in Karlin andAltschul, Proc. Natl. Acad. Sci. USA 90:5873-5877 (1993).

Computer implementations of these mathematical algorithms can beutilized for comparison of sequences to determine sequence identityand/or similarity. Such implementations include, for example: CLUSTAL inthe PC/Gene program (available from Intelligenetics, Mountain View,Calif.); the AlignX program, version 10.3.0 (Invitrogen, Carlsbad,Calif.) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the WisconsinGenetics Software Package, Version 8 (available from Genetics ComputerGroup (GCG), 575 Science Drive, Madison, Wis., USA). Alignments usingthese programs can be performed using the default parameters. TheCLUSTAL program is well described by Higgins et al. Gene 73:237-244(1988); Higgins et al. CABIOS 5:151-153 (1989); Corpet et al., NucleicAcids Res. 16:10881-90 (1988); Huang et al. CABIOS 8:155-65 (1992); andPearson et al., Meth. Mol. Biol. 24:307-331 (1994). The BLAST programsof Altschul et al. J. Mol. Biol. 215:403-410 (1990) are based on thealgorithm of Karlin and Altschul (1990) supra.

Polynucleotides homologous to a reference sequence can be identified byhybridization to each other under stringent or under highly stringentconditions. Single stranded polynucleotides hybridize when theyassociate based on a variety of well characterized physical-chemicalforces, such as hydrogen bonding, solvent exclusion, base stacking andthe like. The stringency of a hybridization reflects the degree ofsequence identity of the nucleic acids involved, such that the higherthe stringency, the more similar are the two polynucleotide strands.Stringency is influenced by a variety of factors, including temperature,salt concentration and composition, organic and non-organic additives,solvents, etc. present in both the hybridization and wash solutions andincubations (and number thereof), as described in more detail inreferences cited below (e.g., Sambrook et al., Molecular Cloning: ALaboratory Manual, 2nd Ed., Vol. 1-3, Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y. (“Sambrook”) (1989); Berger and Kimmel, Guideto Molecular Cloning Techniques, Methods in Enzymology, vol. 152Academic Press, Inc., San Diego, Calif. (“Berger and Kimmel”) (1987);and Anderson and Young, “Quantitative Filter Hybridisation.” In: Hamesand Higgins, ed., Nucleic Acid Hybridisation, A Practical Approach.Oxford, TRL Press, 73-111 (1985)).

Encompassed by the disclosure are polynucleotide sequences that arecapable of hybridizing to the disclosed polynucleotide sequences andfragments thereof under various conditions of stringency (see, forexample, Wahl and Berger, Methods Enzymol. 152: 399-407 (1987); andKimmel, Methods Enzymo. 152: 507-511, (1987)). Full length cDNA,homologs, orthologs, and paralogs of polynucleotides of the presentdisclosure may be identified and isolated using well-knownpolynucleotide hybridization methods.

With regard to hybridization, conditions that are highly stringent, andmeans for achieving them, are well known in the art. See, for example,Sambrook et al. (1989) (supra); Berger and Kimmel (1987) pp. 467-469(supra); and Anderson and Young (1985)(supra).

Hybridization experiments are generally conducted in a buffer of pHbetween 6.8 to 7.4, although the rate of hybridization is nearlyindependent of pH at ionic strengths likely to be used in thehybridization buffer (Anderson and Young (1985)(supra)). In addition,one or more of the following may be used to reduce non-specifichybridization: sonicated salmon sperm DNA or another non-complementaryDNA, bovine serum albumin, sodium pyrophosphate, sodium dodecylsulfate(SDS), polyvinyl-pyrrolidone, ficoll and Denhardt's solution. Dextransulfate and polyethylene glycol 6000 act to exclude DNA from solution,thus raising the effective probe DNA concentration and the hybridizationsignal within a given unit of time. In some instances, conditions ofeven greater stringency may be desirable or required to reducenon-specific and/or background hybridization. These conditions may becreated with the use of higher temperature, lower ionic strength andhigher concentration of a denaturing agent such as formamide.

Stringency conditions can be adjusted to screen for moderately similarfragments such as homologous sequences from distantly related organisms,or to highly similar fragments such as genes that duplicate functionalenzymes from closely related organisms. The stringency can be adjustedeither during the hybridization step or in the post-hybridizationwashes. Salt concentration, formamide concentration, hybridizationtemperature and probe lengths are variables that can be used to alterstringency. As a general guideline, high stringency is typicallyperformed at T_(m)-5° C. to T_(m)-20° C., moderate stringency atT_(m)-20° C. to T_(m)-35° C. and low stringency at T_(m)-35° C. toT_(m)-50° C. for duplex >150 base pairs. Hybridization may be performedat low to moderate stringency (25-50° C. below T_(m)), followed bypost-hybridization washes at increasing stringencies. Maximum rates ofhybridization in solution are determined empirically to occur atT_(m)-25° C. for DNA-DNA duplex and T_(m)-15° C. for RNA-DNA duplex.Optionally, the degree of dissociation may be assessed after each washstep to determine the need for subsequent, higher stringency wash steps.

High stringency conditions may be used to select for nucleic acidsequences with high degrees of identity to the disclosed sequences. Anexample of stringent hybridization conditions obtained in a filter-basedmethod such as a Southern or northern blot for hybridization ofcomplementary nucleic acids that have more than 100 complementaryresidues is about 5° C. to 20° C. lower than the thermal melting point(T_(m)) for the specific sequence at a defined ionic strength and pH.

Hybridization and wash conditions that may be used to bind and removepolynucleotides with less than the desired homology to the nucleic acidsequences or their complements of the present disclosure include, forexample: 6×SSC and 1% SDS at 65° C.; 50% formamide, 4×SSC at 42° C.;0.5×SSC to 2.0×SSC, 0.1% SDS at 50° C. to 65° C.; or 0.1×SSC to 2×SSC,0.1% SDS at 50° C.-65° C.; with a first wash step of, for example, 10minutes at about 42° C. with about 20% (v/v) formamide in 0.1×SSC, andwith, for example, a subsequent wash step with 0.2×SSC and 0.1% SDS at65° C. for 10, 20 or 30 minutes.

For identification of less closely related homologs, wash steps may beperformed at a lower temperature, e.g., 50° C. An example of a lowstringency wash step employs a solution and conditions of at least 25°C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS over 30 min.Greater stringency may be obtained at 42° C. in 15 mM NaCl, with 1.5 mMtrisodium citrate, and 0.1% SDS over 30 min. Wash procedures willgenerally employ at least two final wash steps. Additional variations onthese conditions will be readily apparent to those skilled in the art(see, for example, US Patent Application No. 20010010913).

If desired, one may employ wash steps of even greater stringency,including conditions of 65° C. −68° C. in a solution of 15 mM NaCl, 1.5mM trisodium citrate, and 0.1% SDS, or about 0.2×SSC, 0.1% SDS at 65° C.and washing twice, each wash step of 10, 20 or 30 min in duration, orabout 0.1×SSC, 0.1% SDS at 65° C. and washing twice for 10, 20 or 30min. Hybridization stringency may be increased further by using the sameconditions as in the hybridization steps, with the wash temperatureraised about 3° C. to about 5° C., and stringency may be increased evenfurther by using the same conditions except the wash temperature israised about 6° C. to about 9° C.

Target Nucleic Acids of the Present Disclosure

The recombinant proteins of the present disclosure may be targeted tospecific target nucleic acids to induce gene silencing. The recombinantproteins may be, for example, SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins.

In some embodiments, the SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins are targeted to a specific nucleic acid via a heterologousDNA-binding domain.

In some embodiments, the SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB2/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins reduce expression of a gene of interest by being targeted tothe nucleic acid by a guide RNA.

In some embodiments, the SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB2/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins silence expression of a gene of interest by inducingRNA-directed DNA methylation at the target nucleic acid.

In some embodiments, a target nucleic acid of the present disclosure isa nucleic acid that is located at any location within a target gene thatprovides a suitable location for reducing expression of the target gene.The target nucleic acid may be located within the coding region of atarget gene or upstream or downstream thereof. Moreover, the targetnucleic acid may reside endogenously in a target gene or may be insertedinto the gene, e.g., heterologous, for example, using techniques such ashomologous recombination. For example, a target gene of the presentdisclosure can be operably linked to a control region, such as apromoter, that contains a sequence that can be recognized by acrRNA/tracrRNA and/or a guide RNA of the present disclosure such thatrecombinant proteins of the present disclosure are targeted to thatsequence. Also, the target nucleic acid may be one that is able to bebound by a DNA-binding domain that is recombinantly fused to anepigenetic regulator of the present disclosure. In this sense, a targetnucleic acid of the present disclosure is targeted based on theparticular nucleotide sequence in the target nucleic acid that isrecognized by the targeting portion of the DNA-binding domain, or thecrRNA or guide RNA that is used according to the methods of the presentdisclosure.

In some embodiments, the target nucleic acid is endogenous to the plantwhere the expression of one or more genes is reduced by an epigeneticregulator-like protein (e.g. SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins) of the present disclosure. In some embodiments, the targetnucleic acid is a transgene of interest that has been inserted into aplant. Methods of introducing transgenes into plants are well known inthe art. Transgenes may be inserted into plants in order to provide aproduction system for a desired protein, or may be added to the geneticcompliment in order to modulate the metabolism of a plant.

Examples of suitable endogenous plant genes whose expression can bereduced by an epigenetic regulator-like protein of the presentdisclosure may include, for example, genes that prevent the enhancementof one or more desired traits and genes that prevent increased cropyields. For example, SHH1-like proteins, SHH2-like proteins, AGO4-likeproteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-like proteins,JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-like proteins,NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB10/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1 likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins of the present disclosure may be used to reduce the expressionof the gene GA1 in plants, which would create plants that are lesssensitive to gibberellin. In embodiments relating to research, anepigenetic regulator-like protein of the present disclosure may beutilized to silence the expression of an endogenous gene of interest inorder to generate mutant plants in which to study the function of thegene of interest.

Examples of suitable transgenes present in plants whose expression canbe reduced by an epigenetic regulator-like protein of the presentdisclosure may include, for example, transgenes that are not useful incertain genetic backgrounds, transgenes that are harmful in certaingenetic backgrounds, and transgenes that are expressed in certaintissues that are undesirable. For example, in the case of transgenesthat are expressed in certain tissues that are undesirable, SHH1-likeproteins, SHH2-like proteins, AGO4-like proteins, HDA6-like proteins,NRPD1-like proteins, NRPE1-like proteins, JMJ14-like proteins, RDR2-likeproteins, NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-like proteins,NRPE3B-like proteins, NRPB11/NRPD11/NRPE11-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB12/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1 like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins of the present disclosure can be utilized tosilence the expression of such transgenes in specific tissues atspecific times by operably linking tissue specific promoters to therecombinant polypeptides of the present disclosure. In embodimentsrelating to research, an epigenetic regulator-like protein of thepresent disclosure may be utilized to dynamically study transgenes ofinterest by controlling the induction/silencing of the transgenes.

Suitable target nucleic acids will be readily apparent to one of skillin the art depending on the particular need or outcome. The targetnucleic acid may be in e.g. a region of euchromatin (e.g. highlyexpressed gene), or the target nucleic acid may be in a region ofheterochromatin (e.g. centromere DNA).

Plants of the Present Disclosure

Certain aspects of the present disclosure relate to plants containingone or more epigenetic regulator-like proteins that are targeted to oneor more target nucleic acids in the plant and reduce the expression ofthe one or more target nucleic acids.

As used herein, a “plant” refers to any of various photosynthetic,eukaryotic multi-cellular organisms of the kingdom Plantae,characteristically producing embryos, containing chloroplasts, havingcellulose cell walls and lacking locomotion. As used herein, a “plant”includes any plant or part of a plant at any stage of development,including seeds, suspension cultures, plant cells, embryos, meristematicregions, callus tissue, leaves, roots, shoots, gametophytes,sporophytes, pollen, microspores, and progeny thereof. Also included arecuttings, and cell or tissue cultures. As used in conjunction with thepresent disclosure, plant tissue includes, for example, whole plants,plant cells, plant organs, e.g., leafs, stems, roots, meristems, plantseeds, protoplasts, callus, cell cultures, and any groups of plant cellsorganized into structural and/or functional units.

Any plant cell may be used in the present disclosure so long as itremains viable after being transformed with a sequence of nucleic acids.Preferably, the plant cell is not adversely affected by the transductionof the necessary nucleic acid sequences, the subsequent expression ofthe proteins or the resulting intermediates.

As disclosed herein, a broad range of plant types may be modified toincorporate an epigenetic regulator-like protein of the presentdisclosure. Suitable plants that may be modified include bothmonocotyledonous (monocot) plants and dicotyledonous (dicot) plants.

Examples of suitable plants may include, for example, species of theFamily Gramineae, including Sorghum bicolor and Zea mays; species of thegenera: Cucurbita, Rosa, Vitis, Juglans, Fragaria, Lotus, Medicago,Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium,Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa,Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia,Digitalis, Majorana, Ciahorium, Helianthus, Lactuca, Bromus, Asparagus,Antirrhinum, Heterocallis, Nemesis, Pelargonium, Panieum, Pennisetum,Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Pisum,Phaseolus, Lolium, Oryza, Avena, Hordeum, Secale, and Triticum.

In some embodiments, plant cells may include, for example, those fromcorn (Zea mays), canola (Brassica napus, Brassica rapa ssp.), Brassicaspecies useful as sources of seed oil, alfalfa (Medicago sativa), rice(Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghumvulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet(Panicum miliaceum), foxtail millet (Setaria italica), finger millet(Eleusine coracana)), sunflower (Helianthus annuus), safflower(Carthamus tinctorius), wheat (Triticum aestivum), duckweed (Lemna),soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanumtuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense,Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihotesculenta), coffee (Coffea spp.), coconut (Cocos nucijra), pineapple(Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao),tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana),fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica),olive (Olea europaea), papaya (Carica papaya), cashew (Anacardiumoccidentale), macadamia (Macadamia spp.), almond (Prunus amygdalus),sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley,vegetables, ornamentals, and conifers.

Examples of suitable vegetables plants may include, for example,tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa),green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas(Lathyrus spp.), and members of the genus Cucumis such as cucumber (C.sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).

Examples of suitable ornamental plants may include, for example, azalea(Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus(Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.),daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation(Dianthus caryophyllus), poinsettia (Euphorbiapul cherrima), andchrysanthemum.

Examples of suitable conifer plants may include, for example, loblollypine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinusponderosa), lodgepole pine (Pinus contorta), Monterey pine (Pinusradiata), Douglas-fir (Pseudotsuga menziesii), Western hemlock (Isugacanadensis), Sitka spruce (Picea glauca), redwood (Sequoiasempervirens), silver fir (Abies amabilis), balsam fir (Abies balsamea),Western red cedar (Thuja plicata), and Alaska yellow-cedar(Chamaecyparis nootkatensis).

Examples of suitable leguminous plants may include, for example, guar,locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, limabean, fava bean, lentils, chickpea, peanuts (Arachis sp.), crown vetch(Vicia sp.), hairy vetch, adzuki bean, lupine (Lupinus sp.), trifolium,common bean (Phaseolus sp.), field bean (Pisum sp.), clover (Melilotussp.) Lotus, trefoil, lens, and false indigo.

Examples of suitable forage and turf grass may include, for example,alfalfa (Medicago s sp.), orchard grass, tall fescue, perennialryegrass, creeping bent grass, and redtop.

Examples of suitable crop plants and model plants may include, forexample, Arabidopsis, corn, rice, alfalfa, sunflower, canola, soybean,cotton, peanut, sorghum, wheat, tobacco, and lemna.

The plants of the present disclosure may be genetically modified in thatrecombinant nucleic acids have been introduced into the plants, and assuch the genetically modified plants do not occur in nature. A suitableplant of the present disclosure is one capable of expressing one or morenucleic acid constructs encoding one or more recombinant proteins. Therecombinant proteins encoded by the nucleic acids may be e.g. SHH1-likeproteins, SHH2-like proteins, AGO4-like proteins, HDA6-like proteins,NRPD1-like proteins, NRPE1-like proteins, JMJ14-like proteins, RDR2-likeproteins, NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-like proteins,NRPE3B-like proteins, NRPB11/NRPD11/NRPE11-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB12/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1 like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins.

As used herein, the terms “transgenic plant” and “genetically modifiedplant” are used interchangeably and refer to a plant which containswithin its genome a recombinant nucleic acid. Generally, the recombinantnucleic acid is stably integrated within the genome such that thepolynucleotide is passed on to successive generations. However, incertain embodiments, the recombinant nucleic acid is transientlyexpressed in the plant. The recombinant nucleic acid may be integratedinto the genome alone or as part of a recombinant expression cassette.“Transgenic” is used herein to include any cell, cell line, callus,tissue, plant part or plant, the genotype of which has been altered bythe presence of exogenous nucleic acid including those transgenicsinitially so altered as well as those created by sexual crosses orasexual propagation from the initial transgenic.

“Recombinant nucleic acid” or “heterologous nucleic acid” or“recombinant polynucleotide” as used herein refers to a polymer ofnucleic acids wherein at least one of the following is true: (a) thesequence of nucleic acids is foreign to (i.e., not naturally found in) agiven host cell; (b) the sequence may be naturally found in a given hostcell, but in an unnatural (e.g., greater than expected) amount; or (c)the sequence of nucleic acids contains two or more subsequences that arenot found in the same relationship to each other in nature. For example,regarding instance (c), a recombinant nucleic acid sequence will havetwo or more sequences from unrelated genes arranged to make a newfunctional nucleic acid. Specifically, the present disclosure describesthe introduction of an expression vector into a plant cell, where theexpression vector contains a nucleic acid sequence coding for a proteinthat is not normally found in a plant cell or contains a nucleic acidcoding for a protein that is normally found in a plant cell but is underthe control of different regulatory sequences. With reference to theplant cell's genome, then, the nucleic acid sequence that codes for theprotein is recombinant. A protein that is referred to as recombinantgenerally implies that it is encoded by a recombinant nucleic acidsequence which may be present in the plant cell. Recombinant proteins ofthe present disclosure may also be exogenously supplied directly to hostcells (e.g. plant cells).

A “recombinant” polypeptide, protein, or enzyme of the presentdisclosure, is a polypeptide, protein, or enzyme that is encoded by a“recombinant nucleic acid” or “heterologous nucleic acid” or“recombinant polynucleotide.”

In some embodiments, the genes encoding the recombinant proteins in theplant cell may be heterologous to the plant cell. In certainembodiments, the plant cell does not naturally produce the recombinantproteins, and contains heterologous nucleic acid constructs capable ofexpressing one or more genes necessary for producing those molecules. Incertain embodiments, the plant cell does not naturally produce one ormore polypeptides of the present disclosure, and is provided the one ormore polypeptides through exogenous delivery of the polypeptidesdirectly to the plant cell without the need to express a recombinantnucleic acid encoding the recombinant polypeptide in the plant cell.

Recombinant nucleic acids and/or recombinant proteins of the presentdisclosure may be present in host cells (e.g. plant cells). In someembodiments, recombinant nucleic acids are present in an expressionvector, and the expression vector may be present in host cells (e.g.plant cells).

Expression of Recombinant Proteins in Plants

An epigenetic regulator-like protein of the present disclosure may beintroduced into plant cells via any suitable methods known in the art.For example, an SHH1-like protein, an SHH2-like protein, an AGO4-likeprotein, an HDA6-like protein, an NRPD1-like protein, an NRPE1-likeprotein, a JMJ14-like protein, an RDR2-like protein, anNRPD2A/NRPE2-like protein, an NRPB3/NRPD3/NRPE3A-like protein, anNRPE3B-like protein, an NRPB11/NRPD11/NRPE11-like protein, anNRPB10/NRPD10/NRPE10-like protein, an NRPB12/NRPD12/NRPE12-like protein,an NRPB6A/NRPD6A/NRPE6A-like protein, an NRPB6B/NRPD6B/NRPE6B-likeprotein, an NRPB8A/NRPE8A-like protein, an NRPB8B/NRPD8B/NRPE8B-likeprotein, an NRPE5-like protein, an NRPD4/NRPE4-like protein, anNRPE7-like protein, an NRPD7-like protein, an NRPB5/NRPD5-like protein,an NRPB9A/NRPD9A/NRPE9A-like protein, an NRPB9B/NRPD9B/NRPE9B-likeprotein, an ATRX-like protein, a MOM1-like protein, a MORC1-likeprotein, an SssI-like protein, a DRM2-MTase-like protein, a DNMT3A-likeprotein, a DNMT3L-like protein, a MBD9-like protein, a SUVH2-likeprotein, a SUVH9-like protein, a DMS3-like protein, a MORC6-likeprotein, a SUVR2-like protein, a DRD1-like protein, an RDM1-likeprotein, a DRM3-like protein, a DRM2-like protein, and/or an FRG-likeprotein can be exogenously added to plant cells and the plant cells aremaintained under conditions such that the epigenetic regulator-likeprotein is targeted to one or more target nucleic acids and reduces theexpression of the target nucleic acids in the plant cells.Alternatively, a recombinant nucleic acid encoding an epigeneticregulator-like protein of the present disclosure can be expressed inplant cells and the plant cells are maintained under conditions suchthat the epigenetic regulator-like protein of the present disclosure istargeted to one or more target nucleic acids and reduces the expressionof the target gene in the plant cells. Additionally, in someembodiments, an epigenetic regulator-like protein of the presentdisclosure may be transiently expressed in a plant via viral infectionof the plant, or by introducing an epigenetic regulator-likeprotein-encoding RNA into a plant to temporarily reduce or silence theexpression of a gene of interest. Methods of introducing recombinantproteins via viral infection or via the introduction of RNAs into plantsare well known in the art. For example, Tobacco rattle virus (TRV) hasbeen successfully used to introduce zinc finger nucleases in plants tocause genome modification (“Nontransgenic Genome Modification in PlantCells”, Plant Physiology 154:1079-1087 (2010)).

A recombinant nucleic acid encoding an epigenetic regulator-like proteinof the present disclosure can be expressed in a plant with any suitableplant expression vector. Typical vectors useful for expression ofrecombinant nucleic acids in higher plants are well known in the art andinclude, for example, vectors derived from the tumor-inducing (T1)plasmid of Agrobacterium tumefaciens (e.g., see Rogers et al., Meth. inEnzymol. (1987) 153:253-277). These vectors are plant integratingvectors in that on transformation, the vectors integrate a portion ofvector DNA into the genome of the host plant. Exemplary A. tumefaciensvectors useful herein are plasmids pKYLX6 and pKYLX7 (e.g., see ofSchardl et al., Gene (1987) 61:1-11; and Berger et al., Proc. Natl.Acad. Sci. USA (1989) 86:8402-8406); and plasmid pBI 101.2 that isavailable from Clontech Laboratories, Inc. (Palo Alto, Calif.).

In addition to regulatory domains, an epigenetic regulator-like proteinof the present disclosure can be expressed as a fusion protein that iscoupled to, for example, a maltose binding protein (“MBP”), glutathioneS transferase (GST), hexahistidine, c-myc, or the FLAG epitope for easeof purification, monitoring expression, or monitoring cellular andsubcellular localization.

Moreover, a recombinant nucleic acid encoding an epigeneticregulator-like protein of the present disclosure can be modified toimprove expression of the recombinant protein in plants by using codonpreference. When the recombinant nucleic acid is prepared or alteredsynthetically, advantage can be taken of known codon preferences of theintended plant host where the nucleic acid is to be expressed. Forexample, recombinant nucleic acids of the present disclosure can bemodified to account for the specific codon preferences and GC contentpreferences of monocotyledons and dicotyledons, as these preferenceshave been shown to differ (Murray et al., Nucl. Acids Res. (1989) 17:477-498).

In some embodiments, an epigenetic regulator-like protein of the presentdisclosure can be used to create functional “gene knockout” mutations ina plant by repression of the target gene expression. Repression may beof a structural gene, e.g., one encoding a protein having for exampleenzymatic activity, or of a regulatory gene, e.g., one encoding aprotein that in turn regulates expression of a structural gene.

The present disclosure further provides expression vectors encoding anepigenetic regulator-like protein of the present disclosure (e.g.SHH1-like proteins, SHH2-like proteins, AGO4-like proteins, HDA6-likeproteins, NRPD1-like proteins, NRPE1-like proteins, JMJ14-like proteins,RDR2-like proteins, NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-likeproteins, NRPE3B-like proteins, NRPB11/NRPD11/NRPE1 l-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB2/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1-like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins). A nucleic acid sequence coding for thedesired recombinant nucleic acid of the present disclosure can be usedto construct a recombinant expression vector which can be introducedinto the desired host cell. A recombinant expression vector willtypically contain a nucleic acid encoding a recombinant protein of thepresent disclosure, operably linked to transcriptional initiationregulatory sequences which will direct the transcription of the nucleicacid in the intended host cell, such as tissues of a transformed plant.

For example, plant expression vectors may include (1) a cloned plantgene under the transcriptional control of 5′ and 3′ regulatory sequencesand (2) a dominant selectable marker. Such plant expression vectors mayalso contain, if desired, a promoter regulatory region (e.g., oneconferring inducible or constitutive, environmentally- ordevelopmentally-regulated, or cell- or tissue-specific/selectiveexpression), a transcription initiation start site, a ribosome bindingsite, an RNA processing signal, a transcription termination site, and/ora polyadenylation signal.

A plant promoter, or functional fragment thereof, can be employed tocontrol the expression of a recombinant nucleic acid of the presentdisclosure in regenerated plants. The selection of the promoter used inexpression vectors will determine the spatial and temporal expressionpattern of the recombinant nucleic acid in the modified plant, e.g., thenucleic acid encoding the epigenetic regulator-like protein of thepresent disclosure is only expressed in the desired tissue or at acertain time in plant development or growth. Certain promoters willexpress recombinant nucleic acids in all plant tissues and are activeunder most environmental conditions and states of development or celldifferentiation (i.e., constitutive promoters). Other promoters willexpress recombinant nucleic acids in specific cell types (such as leafepidermal cells, mesophyll cells, root cortex cells) or in specifictissues or organs (roots, leaves or flowers, for example) and theselection will reflect the desired location of accumulation of the geneproduct. Alternatively, the selected promoter may drive expression ofthe recombinant nucleic acid under various inducing conditions.

Examples of suitable constitutive promoters may include, for example,the core promoter of the Rsyn7, the core CaMV 35S promoter (Odell etal., Nature (1985) 313:810-812), CaMV 19S (Lawton et al., 1987), riceactin (Wang et al., 1992; U.S. Pat. No. 5,641,876; and McElroy et al.,Plant Cell (1985) 2:163-171); ubiquitin (Christensen et al., Plant Mol.Biol. (1989)12:619-632; and Christensen et al., Plant Mol. Biol. (1992)18:675-689), pEMU (Last et al., Theor. Appl. Genet. (1991) 81:581-588),MAS (Velten et al., EMBO J. (1984) 3:2723-2730), nos (Ebert et al.,1987), Adh (Walker et al., 1987), the P- or 2′-promoter derived fromT-DNA of Agrobacterium tumefaciens, the Smas promoter, the cinnamylalcohol dehydrogenase promoter (U.S. Pat. No. 5,683,439), the Nospromoter, the pEmu promoter, the rubisco promoter, the GRP 1-8 promoter,and other transcription initiation regions from various plant genesknown to those of skilled artisans, and constitutive promoters describedin, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121;5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5, 608,142.

Examples of suitable tissue specific promoters may include, for example,the lectin promoter (Vodkin et al., 1983; Lindstrom et al., 1990), thecorn alcohol dehydrogenase 1 promoter (Vogel et al., 1989; Dennis etal., 1984), the corn light harvesting complex promoter (Simpson, 1986;Bansal et al., 1992), the corn heat shock protein promoter (Odell etal., Nature (1985) 313:810-812; Rochester et al., 1986), the pea smallsubunit RuBP carboxylase promoter (Poulsen et al., 1986; Cashmore etal., 1983), the Ti plasmid mannopine synthase promoter (Langridge etal., 1989), the Ti plasmid nopaline synthase promoter (Langridge et al.,1989), the petunia chalcone isomerase promoter (Van Tunen et al., 1988),the bean glycine rich protein 1 promoter (Keller et al., 1989), thetruncated CaMV 35s promoter (Odell et al., Nature (1985) 313:810-812),the potato patatin promoter (Wenzler et al., 1989), the root cellpromoter (Conkling et al., 1990), the maize zein promoter (Reina et al.,1990; Kriz et al., 1987; Wandelt and Feix, 1989; Langridge and Feix,1983; Reina et al., 1990), the globulin-1 promoter (Belanger and Kriz etal., 1991), the c-tubulin promoter, the cab promoter (Sullivan et al.,1989), the PEPCase promoter (Hudspeth & Grula, 1989), the R genecomplex-associated promoters (Chandler et al., 1989), and the chalconesynthase promoters (Franken et al., 1991).

Alternatively, the plant promoter can direct expression of a recombinantnucleic acid of the present disclosure in a specific tissue or may beotherwise under more precise environmental or developmental control.Such promoters are referred to here as “inducible” promoters.Environmental conditions that may affect transcription by induciblepromoters include, for example, pathogen attack, anaerobic conditions,or the presence of light. Examples of inducible promoters include, forexample, the AdhI promoter which is inducible by hypoxia or cold stress,the Hsp70 promoter which is inducible by heat stress, and the PPDKpromoter which is inducible by light. Examples of promoters underdevelopmental control include, for example, promoters that initiatetranscription only, or preferentially, in certain tissues, such asleaves, roots, fruit, seeds, or flowers. An exemplary promoter is theanther specific promoter 5126 (U.S. Pat. Nos. 5,689,049 and 5,689,051).The operation of a promoter may also vary depending on its location inthe genome. Thus, an inducible promoter may become fully or partiallyconstitutive in certain locations.

Moreover, any combination of a constitutive or inducible promoter, and anon-tissue specific or tissue specific promoter may be used to controlthe expression of an epigenetic regulator-like protein of the presentdisclosure.

Both heterologous and endogenous promoters can be employed to directexpression of recombinant nucleic acids of the present disclosure.Accordingly, in certain embodiments, expression of a nucleic acidencoding an epigenetic regulator-like protein of the present disclosureis under the control of its respective endogenous promoter. In otherembodiments, expression of a nucleic acid encoding an epigeneticregulator-like protein of the present disclosure is under the control ofa heterologous promoter. Additionally, an endogenous gene encoding foran epigenetic regulator of the present disclosure (e.g. SHH1, SHH2,AGO4, HDA6, NRPD1, NRPE1, JMJ14, RDR2, NRPD2A/NRPE2, NRPB3/NRPD3/NRPE3A,NRPE3B, NRPB11/NRPD11/NRPE11, NRPB10/NRPD10/NRPE10,NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A, NRPB6B/NRPD6B/NRPE6B,NRPB8A/NRPE8A, NRPB8B/NRPD8B/NRPE8B, NRPE5, NRPD4/NRPE4, NRPE7, NRPD7,NRPB5/NRPD5, NRPB9A/NRPD9A/NRPE9A, NRPB9B/NRPD9B/NRPE9B, ATRX, MOM1,MORC1, SssI, DRM2-MTase, DNMT3A, DNMT3L, MBD9, SUVH2, SUVH9, DMS3,MORC6, SUVR2, DRD1, RDM1, DRM3, DRM2, and/or FRG) can be modified usinga knock-in approach, so that the modified gene will be under the controlof its respective endogenous elements. Alternatively, a modified form ofan entire epigenetic regulator genomic sequence may be introduced into aplant, so that the modified/recombinant gene will be under the controlof its endogenous elements and the wild-type gene remains intact. Any orall of these techniques may also be combined to direct the expression ofa recombinant nucleic acid of the present disclosure.

The recombinant nucleic acids of the present disclosure and/or a vectorhousing a recombinant nucleic acid of the present disclosure, may alsocontain a regulatory sequence that serves as a 3′ terminator sequence.One of skill in the art would readily recognize a variety of terminatorsthat may be used in the recombinant nucleic acids of the presentdisclosure. For example, a recombinant nucleic acid of the presentdisclosure may contain a 3′ NOS terminator. Further, a native terminatorfrom an epigenetic regulator of the present disclosure may also be usedin the recombinant nucleic acids of the present disclosure.

Plant transformation protocols as well as protocols for introducingrecombinant nucleic acids of the present disclosure into plants may varydepending on the type of plant or plant cell, e.g., monocot or dicot,targeted for transformation. Suitable methods of introducing recombinantnucleic acids of the present disclosure into plant cells and subsequentinsertion into the plant genome include, for example, microinjection(Crossway et al., Biotechniques (1986) 4:320-334), electroporation(Riggs et al., Proc. Natl. Acad Sci. USA (1986) 83:5602-5606),Agrobacterium-mediated transformation (U.S. Pat. No. 5,563,055), directgene transfer (Paszkowski et al., EMBO J. (1984) 3:2717-2722), andballistic particle acceleration (U.S. Pat. No. 4,945,050; Tomes et al.(1995). “Direct DNA Transfer into Intact Plant Cells via MicroprojectileBombardment,” in Plant Cell, Tissue, and Organ Culture: FundamentalMethods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); and McCabeet al., Biotechnology (1988) 6:923-926).

Additionally, an epigenetic regulator-like protein of the presentdisclosure can be targeted to a specific organelle within a plant cell.Targeting can be achieved by providing the recombinant protein with anappropriate targeting peptide sequence. Examples of such targetingpeptides include, for example, secretory signal peptides (for secretionor cell wall or membrane targeting), plastid transit peptides,chloroplast transit peptides, mitochondrial target peptides, vacuoletargeting peptides, nuclear targeting peptides, and the like (e.g., seeReiss et al., Mol. Gen. Genet. (1987) 209(1):116-121; Settles andMartienssen, Trends Cell Biol (1998) 12:494-501; Scott et al., J BiolChem (2000) 10:1074; and Luque and Correas, J Cell Sci (2000)113:2485-2495).

The modified plant may be grown into plants in accordance withconventional ways (e.g., see McCormick et al., Plant Cell. Reports(1986) 81-84.). These plants may then be grown, and pollinated witheither the same transformed strain or different strains, with theresulting hybrid having the desired phenotypic characteristic. Two ormore generations may be grown to ensure that the subject phenotypiccharacteristic is stably maintained and inherited and then seedsharvested to ensure the desired phenotype or other property has beenachieved.

Methods of Reducing Gene Expression in Plants

Growing conditions sufficient for the recombinant polypeptides of thepresent disclosure to be expressed in the plant to be targeted to andreduce the expression of one or more target nucleic acids of the presentdisclosure are well known in the art and include any suitable growingconditions disclosed herein. Typically, the plant is grown underconditions sufficient to express a recombinant polypeptide of thepresent disclosure (e.g. SHH1-like proteins, SHH2-like proteins,AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins, NRPE1-likeproteins, JMJ14-like proteins, RDR2-like proteins, NRPD2A/NRPE2-likeproteins, NRPB3/NRPD3/NRPE3A-like proteins, NRPE3B-like proteins,NRPB11/NRPD11/NRPE11-like proteins, NRPB0/NRPD10/NRPE10-like proteins,NRPB12/NRPD12/NRPE12-like proteins, NRPB6A/NRPD6A/NRPE6A-like proteins,NRPB6B/NRPD6B/NRPE6B-like proteins, NRPB8A/NRPE8A-like proteins,NRPB8B/NRPD8B/NRPE8B-like proteins, NRPE5-like proteins,NRPD4/NRPE4-like proteins, NRPE7-like proteins, NRPD7-like proteins,NRPB5/NRPD5-like proteins, NRPB9A/NRPD9A/NRPE9A-like proteins,NRPB9B/NRPD9B/NRPE9B-like proteins, ATRX-like proteins, MOM1-likeproteins, MORC1-like proteins, SssI-like proteins, DRM2-MTase-likeproteins, DNMT3A-like proteins, DNMT3L-like proteins, MBD9-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins), and for the expressed recombinant polypeptide to be localizedto the nucleus of cells of the plant in order to be targeted to andreduce the expression of the target nucleic acids. Generally, theconditions sufficient for the expression of the recombinant polypeptidewill depend on the promoter used to control the expression of therecombinant polypeptide. For example, if an inducible promoter isutilized, expression of the recombinant polypeptide in a plant willrequire that the plant to be grown in the presence of the inducer.

As noted above, growing conditions sufficient for the recombinantpolypeptides of the present disclosure to be expressed in the plant tobe targeted to and reduce the expression of one or more target nucleicacids may vary depending on a number of factors (e.g. species of plant,use of inducible promoter, etc.). Suitable growing conditions mayinclude, for example, ambient environmental conditions, standardgreenhouse conditions, growth in long days under standard environmentalconditions (e.g. 16 hours of light, 8 hours of dark), growth in 12 hourlight: 12 hour dark day/night cycles, etc.

Various time frames may be used to observe reduction in expressionand/or targeted methylation of a target nucleic acid according to themethods of the present disclosure. Plants may be observed/assayed forreduction in expression and/or targeted methylation of a target nucleicacid after, for example, about 5 days of growth, about 10 days ofgrowth, about 15 days after growth, about 20 days after growth, about 25days after growth, about 30 days after growth, about 35 days aftergrowth, about 40 days after growth, about 50 days after growth, or 55days or more of growth.

Silencing induced by targeting various recombinant proteins of thepresent disclosure such as, for example, SHH1-like proteins, SHH2-likeproteins, AGO4-like proteins, HDA6-like proteins, NRPD1-like proteins,NRPE1-like proteins, JMJ14-like proteins, RDR2-like proteins,NRPD2A/NRPE2-like proteins, NRPB3/NRPD3/NRPE3A-like proteins,NRPE3B-like proteins, NRPB1/NRPD11/NRPE1 l-like proteins,NRPB10/NRPD10/NRPE10-like proteins, NRPB12/NRPD12/NRPE12-like proteins,NRPB6A/NRPD6A/NRPE6A-like proteins, NRPB6B/NRPD6B/NRPE6B-like proteins,NRPB8A/NRPE8A-like proteins, NRPB8B/NRPD8B/NRPE8B-like proteins,NRPE5-like proteins, NRPD4/NRPE4-like proteins, NRPE7-like proteins,NRPD7-like proteins, NRPB5/NRPD5-like proteins,NRPB9A/NRPD9A/NRPE9A-like proteins, NRPB9B/NRPD9B/NRPE9B-like proteins,ATRX-like proteins, MOM1-like proteins, MORC1-like proteins, SssI-likeproteins, DRM2-MTase-like proteins, DNMT3A-like proteins, DNMT3L-likeproteins, MBD9-like proteins, SUVH2-like proteins, SUVH9-like proteins,DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins, DRD1-likeproteins, RDM1-like proteins, DRM3-like proteins, DRM2-like proteins,and/or FRG-like proteins, can be stable in plants even in the absence ofthese recombinant proteins. Accordingly, the methods of the presentdisclosure may allow one or more target nucleic acids in a plant toremain silenced after the recombinant polynucleotides and/or recombinantpolypeptides of the present disclosure encoding epigeneticregulator-like proteins have been crossed out of the plant. For example,after targeting a particular genomic region with a recombinant proteinaccording to the methods of the present disclosure, the silencing andDNA methylation of the targeted region may remain stable even aftercrossing away the transgenes or after the recombinant polypeptide isotherwise removed from the plant. It is an object of the presentdisclosure to provide plants having reduced expression of one or moretarget nucleic acids according to the methods of the present disclosure.As the methods of the present disclosure may allow one or more targetnucleic acids in a plant to remain silenced after the recombinantpolynucleotides of the present disclosure have been crossed out of theplant or the recombinant polypeptides are otherwise removed from theplant, the progeny plants of these plants may have reduced expression ofone or more target nucleic acids even in the absence of the recombinantpolypeptides or the recombinant polynucleotides that produce therecombinant polypeptides of the present disclosure.

A target nucleic acid of the present disclosure in a plant cell housingan epigenetic-regulator like protein of the present disclosure may haveits level of methylation increased by at least about 5%, at least about10%, at least about 15%, at least about 20%, at least about 25%, atleast about 30%, at least about 40%, at least about 50%, at least about55%, at least about 60%, at least about 65%, at least about 70%, atleast about 75%, at least about 80%, at least about 85%, at least about90%, at least about 91%, at least about 92%, at least about 93%, atleast about 94%, at least about 95%, at least about 96%, at least about97%, at least about 98%, at least about 99%, or at least about 100% ascompared to a corresponding control. Various controls will be readilyapparent to one of skill in the art. For example, a control may be acorresponding plant or plant cell that does not contain a nucleic acidencoding an epigenetic regulator-like protein of the present disclosure.

A target nucleic acid of the present disclosure having increasedmethylation as compared to a corresponding control nucleic acid mayexhibit an increase in methylation over a number of nucleotidesincluding and adjacent to the targeted nucleotide sequences in a targetnucleic acid. For example, the increase in methylation may be presentover one nucleotide, over about 5 nucleotides, over about 10nucleotides, over about 15 nucleotides, over about 20 nucleotides, overabout 25 nucleotides, over about 30 nucleotides, over about 35nucleotides, over about 40 nucleotides, over about 45 nucleotides, overabout 50 nucleotides, over about 55 nucleotides, over about 60nucleotides, over about 75 nucleotides, over about 100 nucleotides, overabout 125 nucleotides, over about 150 nucleotides, over about 175nucleotides, over about 200 nucleotides, over about 225 nucleotides,over about 250 nucleotides, over about 275 nucleotides, over about 300nucleotides, over about 350 nucleotides, over about 400 nucleotides,over about 450 nucleotides, over about 500 nucleotides, over about 600nucleotides, over about 700 nucleotides, over about 800 nucleotides,over about 900 nucleotides, over about 1,000 nucleotides, over about1,500 nucleotides, over about 2,000 nucleotides, over about 2,500nucleotides, or over about 3,000 nucleotides or more as compared tocorresponding nucleotides in a corresponding control nucleic acid. Theincrease in methylation of nucleotides adjacent to the targetnucleotides in the target nucleic acid may occur in nucleotides that are5′ to the target nucleotide sequences, 3′ to the target nucleotidessequences, or both 5′ and 3′ to the target nucleotide sequences.

A target nucleic acid of the present disclosure in a plant cell housingan epigenetic-regulator like protein of the present disclosure may haveits expression reduced by at least about 5%, at least about 10%, atleast about 15%, at least about 20%, at least about 25%, at least about30%, at least about 40%, at least about 50%, at least about 55%, atleast about 60%, at least about 65%, at least about 70%, at least about75%, at least about 80%, at least about 85%, at least about 90%, atleast about 91%, at least about 92%, at least about 93%, at least about94%, at least about 95%, at least about 96%, at least about 97%, atleast about 98%, at least about 99%, or at least about 100% as comparedto a corresponding control. Various controls will be readily apparent toone of skill in the art. For example, a control may be a correspondingplant or plant cell that does not contain a nucleic acid encoding anepigenetic regulator-like protein of the present disclosure.

It is to be understood that while the present disclosure has beendescribed in conjunction with the preferred specific embodimentsthereof, the foregoing description is intended to illustrate and notlimit the scope of the present disclosure. Other aspects, advantages,and modifications within the scope of the present disclosure will beapparent to those skilled in the art to which the present disclosurepertains.

EXAMPLES

The following examples are offered to illustrate provided embodimentsand are not intended to limit the scope of the present disclosure.

Example 1: DNA-Binding Domain-Targeting of Epigenetic Regulators to theFWA Locus

This Example demonstrates the targeting of different epigeneticregulators/components of the RNA-directed DNA methylation pathway torecruit Pol IV and/or Pol V to specific loci.

INTRODUCTION

The RNA-directed DNA methylation (RdDM) pathway mediates de novo DNAmethylation in plants. Applicants have previously demonstrated the useof ZF-SUVH2 to specifically target methylation and silencing of a targetlocus. SUVH2 is an epigenetic regulator and is involved in theRNA-directed DNA methylation pathway. This result was achieved byutilizing the FWA gene as a target. Expression of FWA causes a stronglate-flowering phenotype in Arabidopsis. Methylation at the promoter ofthis gene, as is present in wild-type plants, causes transcriptionalsilencing of FWA and results in an early-flowering phenotype relative tofwa-4 mutants. The fwa-4 Arabidopsis epigenetic mutant shows nomethylation in the promoter of the FWA gene and thus shows thecharacteristic late-flowering phenotype (relative to wild type).Applicants constructed a chimeric SUVH2 protein fused to a Zinc Finger(ZF) protein designed to target the promoter of FWA in Arabidopsis,ZF108, and demonstrates that this fusion protein can promote methylationat this genomic site in fwa-4 plants (See WO/2014/134567). Thismethylation targeting is accompanied by the recruitment of Pol V to this(FWA) site and results in the production of the non-coding RNA needed totrigger methylation, gene silencing, and therefore produce anearly-flowering phenotype.

In this Example, Applicants explored whether other epigenetic regulatorscould be targeted to a specific locus and induce silencing, using theFWA gene as a target locus.

Materials and Methods

Plasmid Construction

In order to create the different fusion proteins described in thisexample, the ZF108 fragment in the pUC57 plasmid was digested with therestriction enzyme XhoI and inserted directly into the unique XhoI sitein different genes or inserted into the unique XhoI of a set of modifiedpCR2 plasmids containing either BLRP_3×Flag, 3×Flag_BLRP, BLRP_3×HA or3×HA_BLRP tags, where the XhoI unique restriction site is locatedbetween the BLRP sequence and the Flag or HA tag, no matter whether Flagor HA tags are in 5′ or 3′ position with respect to the BLRP sequence.ZF108 contains 6 Zn fingers and was designed as described in Segal et al(Segal et al., 2003). ZF108 is designed to target the promoter of FWA inArabidopsis thaliana. The sequence of ZF108 is presented in SEQ ID NO:393. Most of the epigenetic regulator proteins described in this Examplewere from A. thaliana. In addition, the catalytic domain of DRM2 fromNicotiana tabacum was utilized because this domain was successfullycrystalized (Cell, 157: 1050-1060). In addition, the SssI DNAmethyltransferase from the bacteria Spiroplasma sp. was utilized(Nucleic Acids Research, 22:5354-5359).

NRPD1-3×Flag-ZF:

For this purpose, the plasmid pENTR-NRPD1 (Law et al, 2011) was usedthat contains a genomic sequence of NRPD1 including 1450 base pairs of5′ promoter sequence. The 3×Flag-ZF108-BLRP fusion in the pCR2 plasmidwas then digested with AscI and inserted by InFusion (Clontech) in thesingle AscI site of a pENTR-NRPD1 plasmid, located 6 base pairs afterthe end of the coding sequence of NRPD1.

NRPD2-3×Flag-ZF:

For this purpose, the plasmid pDONR-NRPD2 (Haag, J R et al, 2009) wasused that contains a genomic sequence of NRPD2 including 1300 base pairsof 5′ promoter sequence. The NRPD2 sequence was introduced into thevector JP726 by LR reaction (Invitrogen) and the 3×Flag-ZF108-BLRPfusion was cloned into the unique PacI restriction site located 50 bpdownstream of the end of the NRPD2 sequence.

RDR2-3×Flag-ZF:

For this purpose, the plasmid pENTR-RDR2 (Law et al, 2011) was used thatcontains a genomic sequence of RDR2 including 300 base pairs of 5′promoter sequence. The 3×Flag-ZF108-BLRP fusion in the pCR2 plasmid wasinserted in the single AscI site of a pENTR-RDR2 plasmid by InFusion(Clontech), located 6 base pairs after the end of the coding sequence ofRDR2.

SHH1-3×Myc-ZF:

For this purpose, the plasmid pENTR-SHH1 (Law et al, 2011) was used thatcontains a genomic sequence of SHH1 including 1400 base pairs of 5′promoter sequence. A3×Myc-ZF108-BLRP fusion in the pCR2 plasmid was theninserted in the single AscI site of a pENTR-SHH1 plasmid by InFusion(Clontech), located 6 base pairs after the end of the coding sequence ofSHH1. In this particular construction, a shorter ZF108 sequence withonly five tandem copies of the Zn Finger repeats was cloned instead ofthe six tandem copies present in ZF108.

HDA6_3×Flag_ZF:

For this purpose, the plasmid pEG302-HDA6 was used that contains agenomic sequence of HDA6 including 700 base pairs of 5′ promotersequence. The 3×Flag-ZF108-BLRP fusion in the pCR2 plasmid was thendigested with AscI and inserted by InFusion (Clontech) in the singleAscI site of a pEG302-HDA6 plasmid, located 6 base pairs after the endof the coding sequence of HDA6.

ZF-3×Flag-AGO4:

For this purpose, the plasmid pCAMBIA1300a-AGO4 (Li et al, 2006) wasused that contains a genomic sequence of AGO4 including 3700 base pairsof 5′ promoter sequence. The BLRP-ZF108-3×Flag fusion in the pCR2plasmid was then digested with ApaI/BamHI and inserted in the singleApaI/BamHI sites of a pCAMBIA1300a-AGO4 plasmid, located right upstreamof the coding sequence of AGO4.

JMJ14-3×Flag-ZF:

For this purpose, the plasmid pEG302-JMJ14 (Deleris et al, 2010) wasused that contains a genomic sequence of JMJ14 including 1600 base pairsof 5′ promoter sequence. The 3×Flag-ZF108-BLRP fusion in the pCR2plasmid was then digested with AscI and inserted by InFusion (Clontech)in the single AscI sites of a pEG302-JMJ14 plasmid, located 6 base pairsafter the end of the coding sequence of JMJ14.

SHH2_3×FlagZF:

For this purpose, a genomic fragment of SHH2 containing 1294 bp of5′promoter was cloned into pENTR/D (Invitrogen). The 3×Flag-ZF108-BLRPfusion in the pCR2 plasmid was then digested with AscI and inserted byInFusion (Clontech) in the single AscI site of a pENTR-SHH2 plasmid,located 6 base pairs after the end of the coding sequence of SHH2.

ZF_3×Flag_DMS3:

For this purpose, a modified pMDC123 plasmid (Curtis et al, 2003, PlantPhys) was created first, containing 1990 bp of the promoter region ofArabidopis UBQ10 gene upstream of the BLRP_ZF108_3×Flag cassette presentin one of the modified pCR2 plasmids described above. Both UBQ10promoter and BLRP_ZF108_3×Flag are upstream of the gateway cassette(Invitrogen) present in the original pMDC123 plasmid. A cDNA sequence ofDMS3 was cloned first into pENTR/D plasmid (Invitrogen) and thendelivered into the modified pMDC123 by LR reaction (Invitrogen),creating an in-frame fusion of DMS3 cDNA with the upstreamBLRP_ZF_3×Flag cassette.

pUBQ10::ZF_3×Flag_M.SssI.

For this purpose, a modified pMDC123 plasmid (Curtis et al, 2003, PlantPhys) was created first, containing 1990 bp of the promoter region ofArabidopsis UBQ10 gene upstream of the BLRP_ZF108_3×Flag cassettepresent in one of the modified pCR2 plasmids described above. Both UBQ10promoter and BLRP_ZF108_3×Flag are upstream of the gateway cassette(Invitrogen) present in the original pMDC123 plasmid. A plantcodon-optimized cDNA sequence of the Methyltransferase gene fromSpiroplasma sp. strain MQ1 (M.SssI) was cloned first into pENTR/Dplasmid (Invitrogen) and then delivered into the modified pMDC123 by LRreaction (Invitrogen), creating an in-frame fusion of M.SssI cDNA withthe upstream BLRP ZF_3×Flag cassette. The nucleotide sequence of plantcodon-optimized M.SssI in pUBQ10::ZF_3×Flag_M.SssI is set forth as SEQID NO: 661.

pUBQ10::ZF_3×Flag_NtDRM2_Mtase.

For this purpose, a modified pMDC123 plasmid (Curtis et al, 2003, PlantPhys) was created first, containing 1990 bp of the promoter region ofArabidopsis UBQ10 gene upstream of the BLRP_ZF108_3×Flag cassettepresent in one of the modified pCR2 plasmids described above. Both UBQ10promoter and BLRP_ZF108_3×Flag are upstream of the gateway cassette(Invitrogen) present in the original pMDC123 plasmid. A cDNA sequence ofNicotiana tabacum DRM2 methyltransferase domain (NtDRM2_Mtase) wascloned first into pENTR/D plasmid (Invitrogen) and then delivered intothe modified pMDC123 by LR reaction (Invitrogen), creating an in-framefusion of NtDRM2_Mtase cDNA with the upstream BLRP_ZF_3×Flag cassette.The nucleotide sequence of NtDRM2_Mtase inpUBQ10::ZF_3×Flag_NtDRM2_Mtase is set forth as SEQ ID NO: 670.

ZF-3×HA-SUVH9:

For this purpose, the plasmid pENTR-3×HA-SUVH9 (Johnson, L et al, 2008,PLoS Genet. 2008 November; 4 (11):e1000280) was used that contains agenomic sequence of SUVH9 including 1400 base pairs of 5′ promotersequence and a BLRP-3×HA epitope upstream of the start codon. The ZF108in the pCR2 plasmid was then amplified and cloned into the unique XhoIsite of pENTR-3×HA-SUVH9 plasmid. by InFusion (Clontech) creating thepENTR-BLRP-ZF108-3×HA-SUVH9 plasmid.

Plant Transformation

All ZF-108 fusion protein constructs cloned in a pENTR plasmid (seeabove) were recombined into the binary vector pEG302-JP726 by LRreaction (Invitrogen) except for ZF_3×Flag_DMS3,pUBQ10::ZF_3×Flag_M.SssI, pUBQ10::ZF_3×Flag_NtDRM2_Mtase that werecloned in pDMC123 and ZF-3×Flag-AGO4 that was cloned in pCAMBIA1300a.All constructs were introduced into fwa-4 plants usingAgrobacterium-mediated transformation. Transformed lines were selectedusing BASTA, except for ZF-3×Flag-AGO4 where Hygromycin selection wasdone.

Flowering Time Measurements

Flowering time was measured by counting the total number of leaves(rossette and cauline) of each individual plant.

Bisulfite Sequencing and Data Analysis

Bisulfite sequencing followed by PCR amplification and cloning of FWAfragments was done using EZ DNA Methylation-Gold kit (Zymo Research) asperformed in Johnson et al. (2008). BS-Seq libraries were generated aspreviously reported (Cokus et al., 2008) and all libraries weresequenced using the HiSeq 2000 platform following manufacturerinstructions (Illumina) at a length of 50 bp. Bisulfite-Seq (BS-Seq)reads were aligned to the TAIR10 version of the Arabidopsis thalianareference genome using BS-seeker. For BS-Seq up to 2 mismatches wereallowed and only uniquely mapped reads were used.

Results

To explore whether various other RdDM proteins have the ability totrigger de novo DNA methylation at the FWA locus, or otherwise silencethis locus, in the fwa-4 mutant, a series of experiments were conductedin an attempt to target different components of the RdDM pathway to thepromoter of the FWA gene in Arabidopsis. Various proteins involved inRdDM were selected and were fused to the ZF108 zinc finger, whichtargets the FWA promoter (see Materials and Methods), and transformedinto the fwa-4 mutant. ZF-targeting lines were constructed as describedabove. The flowering time of independent transgenic lines was scored.The list of the different RdDM components chosen and the flowering timeresults are shown below in Table 1A.

TABLE 1A Early flowering in T1 lines compared to fwa-4 early late %early SHH1_ZF 13 35 27 SHH2_ZF 4 15 21 ZF_AGO4 12 55 18 HDA6_ZF 3 5 38NRPD1 _ZF 4 13 24 JMJ14_ZF 3 9 25 RDR2_ZF 9 44 14 NRPD2a_ZF 4 24 14ZF_M.SssI 12 16 42 ZF_Mtase 18 31 37 ZF_SUVH9 3 6 33 ZF 0 49 0 2xZF 0 110 YPET_ZF 0 40 0 YPET2x_ZF 0 23 0

The results presented in Table 1A demonstrate that various epigeneticregulators fused to a zinc finger that targets the FWA locus canefficiently promote early flowering in an fwa-4 mutant background.Different proteins also demonstrated a range of ability to induce FWAsilencing. HDA6_ZF had one of the highest silencing efficiencies (38%).

In order to analyze whether the early flowering phenotype of theearly-flowering lines described in Table 1A was due to the methylationof the FWA promoter, a whole-genome bisulfite sequencing assay wasperformed in two independent NRPD1-ZF lines that showed the earlyflowering phenotype relative to fwa-4. Bisulfite sequencing experimentswere conducted as described above. The results, which are presented inFIG. 5, show that DNA methylation was re-established at FWA in theNRPD1-ZF lines. Thus, NRPD1 was effective in targeting methylation atthe FWA promoter. Similar bisulfite sequencing results with otherepigenetic regulator-ZF transgenic lines are presented in FIG. 6. Theseresults suggest that the other epigenetic regulators described abovewhere early flowering was observed may also be targeting DNA methylationto FWA. Regardless of the mechanism, the early flowering phenotypesobserved in transgenic fwa-4 plants is evidence that FWA was silenced.

Applicants have shown that different RdDM proteins can be targeted tosilence specific loci with varying degrees of silencing efficiency.There may be some advantage to having a set of proteins that can providea range of different efficiencies of gene silencing. For example,depending on the target nucleic acid to be silenced, it may beadvantageous to select recombinant proteins of the present disclosurehaving different silencing efficiencies. For example, it may be anadvantage to fully silence the expression of a target gene by selectinga very efficient RdDM component to direct as much methylation aspossible to the target gene. In other cases, it might be an advantage totarget a less efficient RdDM component to target less methylation to agene to cause only a partial silencing effect. Genes often showdifferent effects on plant phenotype when they are expressed atdifferent levels, and there are likely to be situations where partialsilencing of a plant gene is most advantageous.

Example 2: CRISPR-Targeting of Epigenetic Regulators to Specific Loci

This Example describes exemplary experimental guidelines forconstructing fusion constructs containing epigenetic regulators asdisclosed herein fused to dCAS9 proteins. These constructs may be usedto target an epigenetic regulator to a specific locus of a genome usingthe CRISPR-CAS9 system.

To test whether epigenetic regulators as described herein may betargeted to a target nucleic acid using a CRISPR-CAS9 system, a seriesof different fusion constructs will be prepared. As the specificposition of the epigenetic regulator in the fusion protein may impactfunction, different constructs will be prepared such that the epigeneticregulator is oriented either N-terminal or C-terminal to the position ofthe dCAS9 protein in the fusion protein. Different promoters will alsobe tested to evaluate whether certain promoters produce optimalexpression levels of the fusion proteins, such as using constitutivepromoters. Further, in order to ensure optimal functioning of both thedCAS9 protein and the epigenetic regulator, different linkers withdifferent properties will be evaluated in these fusion proteins.

Materials and Methods

Cloning of Fusion Proteins and gRNA-fwa

Exemplary structures of these fusion constructs to be used in theCRISPR-CAS9 system are presented in FIG. 7A, FIG. 7B, FIG. 8A, and FIG.8B. In these figures, different regions of the construct are numericallylabeled, with each region representing a respective module of theconstruct. Fusion constructs containing different variants of themodules presented in these figures will also be prepared, as describedbelow in Table 2A.

TABLE 2A Exemplary Parameters for Fusion Construct Modules TemplateModule Variants DNA 1 pUBI10, pTPL, p35S, endogenous genomic DNA 2dCas9-1xHA-7N-NLS m6UC 3 Flexible (SGGGSGGGGSGGGGS (SEQ ID NO: 865),synthetic GSSGSNGPGGSGGGGSGG (SEQ ID NO: 866), SSGPPPGTG oligo(SEQ ID NO: 867)). Rigid (AEAAAKEAAAKA (SEQ ID NO: 868)).XTEN (SGSETPGTSESATPES (SEQ ID NO: 869)) 3xFlag 4Epigenetic regulator such as e.g. SUVH2, SUVH9, DMS3, cDNAMORC6, SUVR2, DRD1, RDM1, DRM3, DRM2, FRG1, FRG2,SHH1, SHH2, AGO4, HDA6, NRPD1, JMJ14, RDR2, NRPE1,NRPD2A/NRPE2, NRPB3/NRPD3/NRPE3A, NRPE3B,NRPB11/NRPD11/NRPE11, NRPB10/NRPD10/NRPE10,NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A,NRPB6B/NRPD6B/NRPE6B, NRPB8A/NRPE8A,NRPB8B/NRPD8B/NRPE8B, NRPE5, NRPD4/NRPE4, NRPE7, NRPD7, NRPB5/NRPD5,NRPB9A/NRPD9A/NRPE9A, NRPB9B/NRPD9B/NRPE9B,SssI_Mtase, NtDRM2_Mtase, ATRX, MOM1, MORC1, DNMT3A, DNMT3L. 5NOS terminator m6UC 6 TBS Insulator m6UC 7gRNAs with different target sequences gRNA

Exemplary Construct Design

To provide an example, to construct the gRNAs targeting the FWA locus,the binary vector pJRH0646 that contains a plant codon-optimized dCAS9(pdCAS9) driven by the 35S promoter and fused to a 3×Flag tag at theC-terminus will be used. To construct the dCAS9-epigenetic regulatorfusion, a pENTR_D (Invitrogen) plasmid that contains a cDNA fragment ofepigenetic regulator (pENTR_epigenetic regulator) will be used toamplify the epigenetic regulator cDNA, which will be cloned into thepJRH0646 plasmid using appropriate restriction enzymes, immediatelyafter the 3×Flag tag (pJRH0646_35S_pdCAS9_3×Flag_epigenetic regulator).This creates a fusion with pdCAS9 at the N terminus of epigeneticregulator and uses a method similar to the method described in (Gilbertet al., 2013). Features of pJRH0646_35S_pdCAS9_3×Flag_epigeneticregulator include a 35S promoter (SEQ ID NO: 394), NLS_pdCas9_NLS (SEQID NO: 395), flexible linker (SEQ ID NO: 396), 3×FLAG Tag (SEQ ID NO:397), U6 promoter driving expression of gRNA (SEQ ID NO: 398), gRNA-FWAsequence (SEQ ID NO: 399), and the gRNA backbone including the tracrRNAand the gRNA terminator (SEQ ID NO: 400).

All the different modules will be amplified by PCR using specific oligosand cloned into a binary plasmid using InFusion (Clontech)

In order to change the target sequence present in the different gRNAs,the protocol described in Li et al., 2013 will be followed using theplasmid gRNA-m6UC. As an example, to generate the gRNAFWA-8 that targetsthe sequence “gggtttttgcttttcgccat” in the FWA promoter, two consecutivePCRs using the plasmid pUC-gRNA as a template and the oligos12063(GGAAGCTTAGGCCTT AGAAATCTCAAAATTCCGGC (SEQ ID NO: 870)), 12228(atggcgaaaagcaaaaacccAATCACTACTTCGTCTCT (SEQ ID NO: 871)) for PCR1 and12229 (gggtttttgcttttcgccatGTTTTAGAGCTAGAAATAGC (SEQ ID NO: 872)), 12064(GGCAACGCGTrCTAGTAATGCCAACTTTGTACA (SEQ ID NO: 873)) for PCR2 will beperformed.

Alternatively, a tRNA-gRNA expression cassette (Xie, X et al, 2015, ProcNatl Acad Sci USA. 2015 Mar. 17; 112(11):3570-5) will be used to delivermultiple gRNAs simultaneously with high expression level. Due to therepetitive nature of these modules, gene synthesis, instead ortraditional cloning, will be used to generate the cassettes.

To target the FWA locus, various alternative gRNA sequences describedwill be tested, as presented in Table 2B.

TABLE 2B gRNA Molecules Targeting the FWA Promoter crRNA SequencegRNA Name (5′ → 3′) gRNA3 ATTCTCGACGGAAAGATGTA (SEQ ID NO: 874) gRNA4ACGGAAAGATGTATGGGCTT (SEQ ID NO: 875) gRNA14 CCATTGGTCCAAGTGCTATT(SEQ ID NO: 876) gRNA16 GCGGCGCAAGATCTGATATT (SEQ ID NO: 877) gRNA17AAAACTAGGCCATCCATGGA (SEQ ID NO: 878)

Various other loci in the genome will also be targeted to demonstratethe ability of the fusion protein to target a locus of interest.Exemplary loci that will be targeted include GA1, FLC, and RITA. Aseries of different gRNA molecules will be designed that target theseloci. The crRNA portion of these gRNAs are presented below in Table 2C.The gRNA is a fusion of the crRNA and tracrRNA.

TABLE 2C gRNA Molecules Targeting GA1, FLC, or RITA crRNA Sequence LocusgRNA Name (5′ → 3′) GA1 gRNAGA13 GACACACACATACACATACG (SEQ ID NO: 879)gRNAGA14 GCCCTTCAATTCCGTAGCTT (SEQ ID NO: 880) gRNAGA15GGTGGGATCTTCCAAAGCTA (SEQ ID NO: 881) gRNAGA16 GGAGAGAAGGATATGATGCA(SEQ ID NO: 882) gRNAGA17 GACAATCTCTGATGTGAAGT (SEQ ID NO: 883) FLCgRNAFLC1 GTACTATGTAGGCACGACTT (SEQ ID NO: 884) gRNAFLC2GTCAATCCGTATCGTAGGGG (SEQ ID NO: 885) gRNAFLC3 GAGCAAAGACGCTCGTCATG(SEQ ID NO: 886) gRNAFLC4 GGCTCGTCATGCGGTACACG (SEQ ID NO: 887) 8RNAFLC5GCGACTTGAACCCAAACCTG (SEQ ID NO: 888) RITA gRNARITA1GTTCTCGATGTAGTCAGTGG (SEQ ID NO: 889) gRNARITA2 GGGTGGAGCCTCCCTGGAGA(SEQ ID NO: 890) gRNARITA3 GATCAGCTCTGAAGCGGTGA (SEQ ID NO: 891)gRNARITA4 GATGGTGTCTCCTCTCTGAA (SEQ ID NO: 892)

Transformation of fwa-4 Plants

Agrobacterium AGL0 cells will be transformed with the final binaryvector containing the fusion proteins and the gRNA. Arabidopsis fwa-4plants will be transformed using floral dip methods well-known in theart.

Flowering Time Measurements

Progeny of transformed plants (T1s) will be planted and screened forglufosinate-resistant plants that incorporate the T-DNA into theArabidopsis genome, which confers resistance to glufosinate. Among theglufosinate-resistant transgenic plants, flowering time will be measuredand compared to early-flowering wild-type Col0 and late-flowering fwa-4plants. Flowering time will be measured by counting the total number ofleaves (rossette and cauline) of each individual plant.

Data Analysis

Plants transformed with the fusion constructs described above will beevaluated for phenotypic differences as compared to correspondingcontrol plants (e.g. wild-type plants) which are suggestive ofsuccessful fusion protein targeting to the locus of interest andsubsequent silencing at the locus. The phenotype evaluated may varydepending on the locus targeted.

Other analyses to be performed may include measuring the expressionlevel of the targeted locus in the transformed plants, measuring thedegree of DNA methylation at the targeted locus in the transformedplants, or other assays well-known to those of skill in the art.

It is thought that the fusion proteins containing an epigeneticregulator as described herein and a dCAS9 protein will be able tosuccessfully target a locus of interest and induce epigenetic silencing.

Example 3: Modified CRISPR-Targeting of Epigenetic Regulators toSpecific Loci Using MS2 Coat Proteins

This Example describes exemplary experimental guidelines forconstructing recombinant constructs for use in a modifiedCRISPR-targeting scheme involving epigenetic regulators as disclosedherein, dCAS9 proteins, and MS2 coat proteins. These constructs may beused to target an epigenetic regulator to a specific locus of a genomeusing the CRISPR-CAS9 system.

Example 2 describes the recombinant fusing of epigenetic regulatorproteins to a dCAS9 protein to target these epigenetic regulators to thee.g. FWA locus. However, it is possible that in some instances, thefusion between the epigenetic regulator and the dCAS9 protein may impactthe function of the epigenetic regulator, the dCAS9 protein, or both theepigenetic regulator and the dCAS9 protein. One way to circumvent thispotential issue is to use other methods of CRISPR-targeting theepigenetic regulator to the locus of interest other than by fusing theepigenetic regulator to the dCAS9 protein.

One such method involves adding a small RNA sequence that binds to aspecific protein which can then be fused to the epigenetic regulator.Recently, work by Konermann et al. 2014 showed that two loops in thegRNA backbone (tetraloop and stem 2) can be modified without negativeeffects on gRNA-CAS9 activity. They added to these loops a hairpinaptamer that selectively binds dimerized MS2 bacteriophage coat proteinsand showed that MS2-mediated recruitment of the transcriptionalactivator VP64 to the gRNA-CAS9 complex was able to induce expression ofa target gene.

A similar technique will be used herein to bypass the possible negativeeffect that an epigenetic regulator or the CAS9 protein may have on eachother's activity when expressed as a fusion protein. A fusion proteinbetween MS2 and an epigenetic regulator will be constructed. The diagrampresented in FIG. 9 is a representative scheme of this three componentsystem: (CAS9/gRNA-MS2-aptamer/MS2-epigenetic regulator). Exemplaryepigenetic regulators that may be used in this scheme include e.g. SHH1,SHH2, AGO4, HDA6, NRPD1, JMJ14, RDR2, NRPE1, NRPD2A/NRPE2,NRPB3/NRPD3/NRPE3A, NRPE3B, NRPB11/NRPD11/NRPE11, NRPB10/NRPD10/NRPE10,NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A, NRPB6B/NRPD6B/NRPE6B,NRPB8A/NRPE8A, NRPB8B/NRPD8B/NRPE8B, NRPE5, NRPD4/NRPE4, NRPE7, NRPD7,NRPB5/NRPD5, NRPB9A/NRPD9A/NRPE9A, NRPB9B/NRPD9B/NRPE9B, ATRX, MOM1,MORC1, DNMT3A, DNMT3L, DMS3, DRD1, RDM1, DRM3, DRM2, FRG, SUVR2, MORC6,SHH1, SssI MTase, NtDRM2 MTase, SUVH2, and/or SUVH9.

A guide RNA designed to the FWA locus will be fused to the MS2 aptamerto guide the MS2-epigenetic regulator fusion protein to FWA via thedCAS9 protein.

Other RNA-binding proteins may also be used in place of MS2, such as PP7and COM.

By way of example, a detailed summary of an exemplary MS2 fusionconstruct containing NtDRM2 Mtase is provided, described herein asm4UC_dCas9_MS2_NtDRM2_Mtase_gRNAMS2. For this purpose, m4UC_UBQ10_dCas9vector will be used. This vector will contain 2 kb of the 5′ promoter ofArabidopsis UBQ10 gene driving expression of a plant codon-optimizeddCas9 that is fused in its C-terminus to 1×HA tag and 7N NuclearLocalization Signals (NLS). A catalytically inactive Cas9, dCas9, willbe generated by site directed mutagenesis to change D10A and H840 aminoacids. Next, a modified pMDC123 vector (Curtis et al, Plant Phys, 2003)containing 700 bp of the 3′ OCS terminator will be used. 2 kb of UBQ10promoter, the MS2 binding protein sequence containing 3×GGGS flexiblelinker and one NLS (Konermann et al Nature. 2014) and 2×Flag sequencewill be PCR amplified and cloned in this order by Infusion (Clontech)into the unique AscI site upstream of the gateway cassette of themodified pMDC123 to create pMDC123_MS2. The fragment of pMDC123_MS2containing UBQ10 promoter_MS2_GatewayCassette_OCS terminator will be PCRamplified and inserted by InFusion (Clontech) into the unique PmeI siteof m4UC_UBQ10_dCas9 vector to create m4UC_MS2 vector. A pENTR vector(Invitrogen) containing a cDNA of NtDRM2_Mtase will be used to deliverNtDRM2_Mtase into m4UC_MS2 by LR reaction (Invitrogen) to createm4UC_MS2_NtDRM2_Mtase vector. Last, Arabidopsis U6 promoter and a gRNAwith MS2 loops at tetraloop and stemloop 2 (Konermann et al Nature.2014) will be PCR amplified and cloned into the unique PmeI site ofm4UC_MS2_NtDRM2_Mtase vector by Infusion (Clontech). Different 20nt-long gRNA protospacers against FWA promoter will be cloned into thegRNA_MS2 by PCR. Alternatively, a tRNA-gRNA expression cassette (Xie, Xet al, 2015, Proc Natl Acad Sci USA. 2015 Mar. 17; 112(11):3570-5) willbe used.

The nucleotide sequence of m4UC_dCas9_MS2_NtDRM2_Mtase_gRNAMS2 ispresented as SEQ ID NO: 671. This vector also includes the followingfeatures: gRNA (See Table 38), U6 promoter (SEQ ID NO: 415), OCSterminator (SEQ ID NO: 416), UBQ10 promoter (SEQ ID NO: 417), Insulator(SEQ ID NO: 418), and omega enhancer (SEQ ID NO: 419). The polypeptidesequences encoded in this vector include the following: dCas9_HA_7N-NLS(SEQ ID NO: 420), which includes dCas9 (SEQ ID NO: 421), 1×HA (SEQ IDNO: 422), and 7N-NLS (SEQ ID NO: 423); andMS2_3×GGGGS_NLS_2×Flag_NtDRM2_MTase (SEQ ID NO: 424), which includes MS2(SEQ ID NO: 425), 3×GGGGS (SEQ ID NO: 426), NLS (SEQ ID NO: 427), 2×FLAG(SEQ ID NO: 428), and NtDRM2_Mtase (SEQ ID NO: 631).

Arabidopsis fwa-4 plants will be transformed with these constructs andevaluated for flowering time phenotypes as described in Examples 1 and2.

It is thought that the targeting scheme described in this Example willallow the epigenetic regulator to be targeted a locus of interest andinduce epigenetic silencing. Early flowering of fwa-4 plants expressingthese constructs relative to Col-O wild-type plants will serve as aproxy of silencing of the FWA locus. Molecular analysis of the plantswill also be done to analyze methylation status of the target.

Example 4: Modified CRISPR-Targeting of Epigenetic Regulators toSpecific Loci Using SunTag Constructs

This Example describes exemplary experimental guidelines forconstructing recombinant constructs for use in a modifiedCRISPR-targeting scheme involving epigenetic regulators as disclosedherein, dCAS9 proteins, and SunTag constructs. These constructs may beused to target an epigenetic regulator to a specific locus of a genomeusing the CRISPR-CAS9 system.

Example 2 describes the recombinant fusing of epigenetic regulatorproteins to a dCAS9 protein to target these epigenetic regulators to theFWA locus. However, it is possible that in some instances, the fusionbetween the epigenetic regulator and the dCAS9 protein may impact thefunction of the epigenetic regulator, the dCAS9 protein, or both theepigenetic regulator and the dCAS9 protein. Further, previous work withCRISPR targeting has demonstrated that fusing a protein of interest to aCAS9 protein results in variable abilities to target transcriptionalregulation of a locus of interest. Normally, a single copy of a proteinhas been fused to either the N- or C-terminal portion of CAS9. One wayto circumvent these potential issues is to use other methods ofCRISPR-targeting the epigenetic regulator to the locus of interest otherthan by fusing the epigenetic regulator to the dCAS9 protein.

Recently, a technique called SunTag was developed to recruit manyeffector proteins simultaneously to a location via one dCAS9 protein. Inthis way, there is an amplification of the effect of targeting, andimproved magnitude of gene regulation (Tanenbaum et al, 2014). Tanenbaumet al. described that a dCas9 protein was fused to an unstructuredpeptide that contains up to 24 copies of the GCN4 epitope. A singlechain antibody, scFV, designed to bind this peptide sequence with highaffinity and specificity, was fused to an effector protein for generegulation. Co-expression of the two components allows binding of up to24 copies of the antibody-fused effector protein to each CAS9-GCN4fusion protein. In the case of VP64 as an effector protein, thisprocedure resulted in very high activation of gene expression comparedto simple CAS9-VP64 fusion proteins.

A similar technique will be used herein to allow e.g. 10-24 copies of anepigenetic regulator to bind a dCAS9-GCN4 fusion protein. The targetingscheme described in this Example will use a dCAS9-GCN4 fusion similar tothat described by Tanenbaum above, but will also involve expressing afusion of an epigenetic regulator to the scFV antibody. The diagrampresented in FIG. 10 is a representative scheme of this targetingsystem. Exemplary epigenetic regulators that may be used in this schemeinclude e.g. SHH1, SHH2, AGO4, HDA6, NRPD1, JMJ14, RDR2, NRPE1,NRPD2A/NRPE2, NRPB3/NRPD3/NRPE3A, NRPE3B, NRPB11/NRPD11/NRPE11,NRPB10/NRPD10/NRPE10, NRPB12/NRPD12/NRPE12, NRPB6A/NRPD6A/NRPE6A,NRPB6B/NRPD6B/NRPE6B, NRPB8A/NRPE8A, NRPB8B/NRPD8B/NRPE8B, NRPE5,NRPD4/NRPE4, NRPE7, NRPD7, NRPB5/NRPD5, NRPB9A/NRPD9A/NRPE9A,NRPB9B/NRPD9B/NRPE9B, ATRX, MOM1, MORC1, DNMT3A, DNMT3L, DMS3, DRD1,RDM1, DRM3, DRM2, FRG, SUVR2, MORC6, SHH1, SssI MTase, NtDRM2 MTase,SUVH2, and/or SUVH9. A guide RNA designed to target the FWA locus willbe co-expressed with the U6 promoter as in the schemes.

By way of example, a detailed summary of an exemplary SunTag fusionconstruct containing DMS3 is provided, described herein asm4UC_dCas9_1×HA_2×NLS_GCN4×10_scFv_sfGFP_DMS3_GB1_REX NLS_gRNA. Forcloning the SunTag construct (Tanenbaum et al., Cell 2014), them4UC_UBQ10 vector will be used. This vector contains ˜2 kb of thepromoter of the Arabidopsis UBQ10 gene. The dCas9_1×HA_2×NLS_GCN4×10fusion will be PCR amplified from one of the original SunTag plasmidsfrom Addgene (pHRdSV40-NLS-dCas9-2×NLS-10×GCN4_V4-NLS-P2A-BFP-NLS-dWPRE,Vale lab). Through the use of two unique restriction sites (HpaI andSmaI), the amplified dCas9 will be inserted into m4UC by In-Fusioncloning (Clontech), such that the UBQ10 promoter drives dCas9expression, and an OCS terminator follows the sequence. Next, by using aunique PmeI site, a UBQ10 promoter (along with unique restriction sitesflanking the promoter) will be inserted into m4UC downstream from a TBSinsulator through In-Fusion cloning. Using another one of the SunTagplasmids from Addgene (pHRdSV40-scFv GCN4-sfGFP-VP64-GB1-Rex_NLS-dWPRE),a series of PCRs will replace VP64 with DMS3 flanked by uniquerestriction sites. The single-chain variable fragment antibody(scFv)+superfolder GFP (sfGFP)+DMS3+GB1+REX NLS PCR amplicon will thenbe cloned into m4UC downstream from the UBQ10 promoter with In-Fusioncloning using a new unique PmeI site. Through subsequent In-Fusioncloning deletions and additions of PmeI sites, a NOS terminator will beinserted downstream from the REX NLS, followed by a U6 promoter drivingthe expression of a gRNA. A unique PmeI site at the end also enables theaddition of multiple U6 promoter driven gRNAs.

The nucleotide sequence ofm4UC_dCas9_1×HA_2×NLS_GCN4×10_scFv_sfGFP_DMS3_GB1_REX NLS_gRNA ispresented as SEQ ID NO: 430. This vector also includes the followingfeatures: UBQ10 promoter (SEQ ID NO: 431), Omega RBC (SEQ ID NO: 432),OCS terminator (SEQ ID NO: 433), TBS insulator (SEQ ID NO: 434), NOSterminator (SEQ ID NO: 435), U6 promoter+gRNA (SEQ ID NO: 436), andprotospacer (SEQ ID NO: 437). The polypeptide sequences encoded in thisvector include the following: Cas9 portion (SEQ ID NO: 438), whichincludes dCas9 (SEQ ID NO: 439), 1×HA (SEQ ID NO: 440), NLS (SEQ ID NO:441), flexible linker (SEQ ID NO: 442), and GCN4×10 (SEQ ID NO: 443), aswell as the antibody portion (SEQ ID NO: 444), which includes scFV (SEQID NO: 445), sfGFP (SEQ ID NO: 446), GGGGG linker (SEQ ID NO: 447), DMS3(SEQ ID NO: 448), GB1 (SEQ ID NO: 449), and REX NLS (SEQ ID NO: 450).

Arabidopsis fwa-4 plants will be transformed with these constructs andevaluated for flowering time phenotypes as described in Examples 1 and2.

It is thought that the targeting scheme described in this Example willallow the epigenetic regulator to be targeted a locus of interest andinduce epigenetic silencing. Early flowering of fwa-4 plants expressingthese constructs relative to Col-O wild-type plants will serve as aproxy of silencing of the FWA locus.

Example 5: In Vivo DNA Methylation and Silencing of a Reporter Transgeneby Transient Expression in Nicotiana benthamiana

This Example demonstrates in vivo DNA methylation and silencing of areporter transgene by transient expression of a targeting construct inNicotiana benthamiana.

In order to test the ability to methylate target sequences in vivo usingthe ZF108- or CRISPR/CAS9-targeted NtDRM2 catalytic domain, a transientexpression assay in N. benthamiana was utilized. Briefly, a reporterconstruct, where the FWA promoter sequence was cloned upstream of thereporter gene Luciferase (LUC), was expressed in N. benthamiana togetherwith a negative control plasmid-GUS-, or with the pMDC_ZF_NtDRM2_Mtaseor the pMDC_dCas9_NtDRM2_Mtase plasmids, including the tRNA-gRNAexpression cassettes (See Materials and Methods). After 3 days,infiltrated leaves were collected and DNA and RNA were extracted inorder to analyze DNA methylation over the FWA promoter and theexpression level of the FWA-driven LUC transgene. After bisulfitetreatment of the different DNA samples, PCR using specific primers fordifferent FWA promoter regions was performed (BS-PCR).

Materials and Methods

Materials and Methods not otherwise detailed in this section can befound in Example 2 above (e.g. specific gRNA sequences).

Cloning of pMDC_dCas9_1×HA_7N-NLS_NtDRM2_Mtase

For this purpose, a modified pMDC123 plasmid (Curtis et al, 2003, PlantPhys) was created first. A fragment containing 1990 bp of the promoterregion of Arabidopsis UBQ10 gene was cloned, followed by a plantcodon-optimized dCas9, containing an omega RBC translational enhancer atthe N-terminus of dCas9 and 1×HA tag followed by a nuclear localizationsignal (NLS) at the C-terminus of dCas9, creatingpMDC_dCas9_1×HA_7N-NLS_Gateway. A cDNA sequence of Nicotiana tabacumDRM2 methyltransferase domain (NtDRM2_Mtase) was cloned first intopENTR/D plasmid (Invitrogen) and then delivered intopMDC_dCas9_1×HA_7N-NLS_Gateway by LR reaction (Invitrogen), creating anin-frame fusion of NtDRM2_Mtase cDNA with the upstream dCas9_1×HA_7N-NLScassette. Two different tRNA-gRNA expression cassettes, one with twodifferent gRNAs and one with four different gRNAs, were created by genesynthesis (SGI-DNA), and inserted at the HindIII restriction site ofpMDC_dCas9_×HA_7N-NLS_NtDRM2_Mtase, upstream of the UBQ10 promotersequence.

The nucleotide sequences of relevant features ofpMDC_dCas9_1×HA_7N-NLS_NtDRM2_Mtase (SEQ ID NO: 634), are set forth,including the UBQ10 promoter (SEQ ID NO: 625), OMEGA enhancer (SEQ IDNO: 626), dCas9 (SEQ ID NO: 627), 1×HA (SEQ ID NO: 628), 7N-NLS (SEQ IDNO: 629), linker (SEQ ID NO: 630), NtDRM2_Mtase cDNA (SEQ ID NO: 631),Terminator (SEQ ID NO: 632). The construct containingpMDC_dCas9_1×HA_7N-NLS_NtDRM2_Mtase also contained the respectivetRNA_gRNA (U6p::tRNA-4-17, SEQ ID NO: 642, or U6p::tRNA-16-14-3-17, SEQID NO: 657).

To target the FWA locus, various alternative gRNA sequences were used inthe tRNA_gRNA expression constructs, as presented in Table 5A.

TABLE 5A Sequence of the different gRNAs used in the tRNA-gRNA expression cassette crRNA Sequence gRNA Name (5′ → 3′) gRNA3ATTCTCGACGGAAAGATGTA (SEQ ID NO: 893) gRNA4 ACGGAAAGATGTATGGGCTT(SEQ ID NO: 894) gRNA14 CCATTGGTCCAAGTGCTATT (SEQ ID NO: 895) gRNA16GCGGCGCAAGATCTGATATT (SEQ ID NO: 896) gRNA17 AAAACTAGGCCATCCATGGA(SEQ ID NO: 897)

Features of pFWA:LUC

The construction of pFWA:LUC is described above. The nucleotide sequenceof pFWA:LUC is set forth as SEQ ID NO: 677.

Transient Expression in N. benthamiana by Agroinfiltration

The following protocol was used for the agroinfiltration procedure:

Day 1

-   -   Inoculate 5 ml LB containing 10 μL of Rif (50 mg/ml) and 5 μL        (50 mg/ml) of Kanamycin using a single agrobacterium colony.    -   Incubate them at 28° C. overnight.

Day 2

-   -   Make 25 ml LB media containing MES (10 mM, pH5.6),        Acetosyringone (20 μM).    -   Use 500 μl from 5 ml LB culture grown overnight to inoculate the        25 ml LB.    -   Incubate them at 28° C. overnight.

Day 3

-   -   Spin down the 25 ml cultures: 20 mins, 4000 rpm, 28° C.    -   Make agroinfiltration buffer (IB) (10 mM MES pH5.6, 10 mM MgCl2,        200 μM Acetosyringone)    -   Re-suspend the pellet in 5 ml of Infiltration buffer (Agro        stock)    -   Use 100 μL from Agro stock to measure the concentration of the        agrobacteria at OD 600. Concentration of Agrobacteria containing        different plasmid was set at 0.5.    -   Incubate for 2 hours at room temperature.    -   Infiltrate 7-8 leaves of 4 week old N. benthamiana. At least 3-4        leaves are collected and pooled for each time point.

Results

Agroinfiltrated leaves with the constructs described above wereanalyzed. Sequencing of the BS-PCR products shows that bothZF_NtDRM2_Mtase and dCas9_NtDRM2_Mtase, driven by gRNA4 and 17, wereable to promote DNA methylation of FWA (FIG. 11), whereas the FWA+GUScontrol was unmethylated. Further, whole genome bisulfite sequencing oftwo representative ZF-NtDRM2_Mtase T1 plants and a Col0 wild-typecontrol revealed robust methylation of the FWA promoter byZF-NtDRM2_Mtase (FIG. 13). This demonstrates that NtDRM2_Mtase can causein vivo de novo DNA methylation when targeted either by artificial ZincFingers or CRISPR/Cas9 to a genomic locus.

In addition, reduced expression levels of the FWA promoter-drivenluciferase transgene (LUC), in samples co-infiltrated withZF_NtDRM2_Mtase and dCas9_NtDRM2_Mtase, (gRNA4 and 17), indicates thattargeted hypermethylation of the FWA promoter is correlated with genesilencing (FIG. 12).

Example 6: CRISPR-Targeting of NtDRM2_Mtase to the FWA Locus inArabidopsis

This Example describes exemplary experimental guidelines forconstructing recombinant constructs for use in a modifiedCRISPR-targeting scheme using a plant codon-optimized CAS9 protein thatcarries two point mutations within the endonuclease domain that isrecombinantly fused to a NtDRM2_Mtase protein (pdCAS9-Mtase), and atRNA-gRNA expression cassette composed of two or four different gRNAstargeting the FWA locus in Arabidopsis. fwa-4 mutant plants harboringpdCAS9-Mtase and guide RNA targeting the FWA locus are expected toexperience early flowering relative to the control fwa-4 line, andmethylation of the FWA sequence.

Materials and Methods

The DNA constructs used in this experiment will be exactly as describedin Example 5.

Transformation of Fwa-4 Plants

Agrobacterium AGL0 cells will be transformed with the plasmids describedabove and Arabidopsis fwa-4 plants will be transformed with thisAgrobacterium strain using the floral dip method which is well known inthe art.

Flowering Time Measurements

Progeny of transformed plants (T1s) will be planted and screened forglufosinate-resistant plants that incorporate the T-DNA into theArabidopsis genome, which confers resistance to glufosinate. Among theglufosinate-resistant transgenic plants, flowering time will be measuredand compared to early-flowering wild-type Col-O and late-flowering fwa-4plants. Flowering time will be measured by counting the total number ofleaves (rossette and cauline) of each individual plant.

FWA Promoter and Expression Analysis

Molecular analysis of the FWA promoter (e.g. methylation status) and FWAexpression levels in plants transformed with the constructs describedabove will be performed as described above.

Example 7: DNA-Binding Domain-Targeting of ATRX, MOM1, and MORC1 to theFWA Locus

This Example demonstrates the targeting of ATRX, MOM1, and MORC1polypeptides to the FWA locus via zinc finger targeting.

Materials and Methods

Recombineering of ATRX-3×FLAG-ZNF108

The sequence of 3×FLAG-ZNF108 was inserted at the 3′ end of the ATRXgenomic sequence in a transformation-competent artificial chromosomeclone using a bacterial recombineering approach (Crawford et al.,Science 347(6222):655-9). This approach results in a cassette in whichATRX is driven by its own endogenous promoter. The accession number ofATRX is AT1G08600.

The nucleotide sequence of the ATRX-3×FLAG-ZNF108 expression cassette ispresented in SEQ ID NO: 720. Features of this cassette include: 5′ UTR(SEQ ID NO: 721), ATRX genomic DNA (SEQ ID NO: 722), linker (SEQ ID NO:723), 3×FLAG (SEQ ID NO: 724), linker (SEQ ID NO: 725), ZNF108 (SEQ IDNO: 726), 3′ UTR (SEQ ID NO: 727). The amino acid sequence ofATRX-3×FLAG-ZNF108 is presented in SEQ ID NO: 728. Features include ATRX(SEQ ID NO: 729), linker (SEQ ID NO: 730), 3×FLAG (SEQ ID NO: 731),linker (SEQ ID NO: 732), and ZNF108 (SEQ ID NO: 733). A schematic of thecassette is presented in FIG. 14A.

Recombineering of MOM1-3×FLAG-ZNF108

The sequence of 3×FLAG-ZNF108 was inserted at the 3′ end of the MOM1genomic sequence in a transformation-competent artificial chromosomeclone using a bacterial recombineering approach (Crawford et al.,Science 347(6222):655-9). This approach results in a cassette in whichMOM1 is driven by its own endogenous promoter. The accession number ofMOM1 is AT1G08060.

The nucleotide sequence of the MOM1-3×FLAG-ZNF108 expression cassette ispresented in SEQ ID NO: 734. Features of this cassette include: 5′ UTR(SEQ ID NO: 735), MOM1 genomic DNA (SEQ ID NO: 736), linker (SEQ ID NO:737), 3×FLAG (SEQ ID NO: 738), linker (SEQ ID NO: 739), ZNF108 (SEQ IDNO: 740), 3′ UTR (SEQ ID NO: 741). The amino acid sequence ofMOM1-3×FLAG-ZNF108 is presented in SEQ ID NO: 742. Features include MOM1(SEQ ID NO: 743), linker (SEQ ID NO: 744), 3×FLAG (SEQ ID NO: 745),linker (SEQ ID NO: 746), and ZNF108 (SEQ ID NO: 747). A schematic of thecassette is presented in FIG. 16A.

Construction of MORC1_Flag_ZF

The 3×Flag-ZF108-BLRP fusion in the pCR2 plasmid was digested with AscIand inserted in the single AscI site of the pENTR-MORC1 plasmid(Moissard et al, 2014), located 6 base pairs after the end of the codingsequence of MORC1 (from A. thaliana). The resulting plasmid wasrecombined into JP726 using LR clonase (Invitrogen) to createpEG302_MORC1_3×Flag_ZF108.

Plant Transformation

All constructs were introduced into fwa-4 plants usingAgrobacterium-mediated transformation. Transformed lines were selectedusing BASTA.

Flowering Time Measurements

Flowering time was measured by counting the total number of leaves(rossette and cauline) of each individual plant.

Bisulfite Sequencing and Data Analysis

Bisulfite sequencing followed by PCR amplification and cloning of FWAfragments was done using EZ DNA Methylation-Gold kit (Zymo Research) asperformed in Johnson et al. (2008). BS-Seq libraries were generatedusing the Ovation Ultralow Methyl-seq Library kit from Nugen, and alllibraries were sequenced using HiSeq sequencers following manufacturerinstructions (Illumina) at a length of 50 bp. Bisulfite-Seq (BS-Seq)reads were aligned to the TAIR10 version of the Arabidopsis thalianareference genome using BS-seeker. For BS-Seq up to 2 mismatches wereallowed and only uniquely mapped reads were used.

Results

To explore whether ATRX, MOM1, and MORC1 have the ability to trigger denovo DNA methylation at the FWA locus, or otherwise silence this locus,in the fwa-4 mutant, a series of experiments were conducted in anattempt to target these polypeptides to the promoter of the FWA gene inArabidopsis. These polypeptides were fused to the ZF108 zinc finger,which targets the FWA promoter (see Example 1), and transformed into thefwa-4 mutant. ZF-targeting lines were constructed as described above.The flowering time of independent transgenic lines was scored.

MORC1-ZF

The flowering time results for MORC1-ZF are shown below in Table 7A.˜57% of the T1 lines analyzed showed early flowering relative to thefwa-4 mutant. The results suggest that MORC1 was able to be targeted tothe FWA locus via ZF-targeting and induce silencing of this locus.

TABLE 7A Early flowering in T1 lines compared to fwa-4 early late %early MORC1-ZF 26 20 57

ATRX-ZF

Flowering time was also analyzed in ATRX-ZF lines. As can be seen inFIG. 14B, two independent T2 lines housing ATRX-ZF are shown thatexhibited early flowering as compared to the fwa mutant. The resultssuggest that ATRX was able to be targeted to the FWA locus viaZF-targeting and induce silencing of this locus.

In order to analyze whether the early flowering phenotype in the ATRX-ZFlines was due to the methylation of the FWA promoter, a bisulfitesequencing assay was performed in independent ATRX-ZF lines that showedthe early flowering phenotype relative to fwa-4. The results, which arepresented in FIG. 15, interestingly show that robust DNA methylation wasnot re-established at FWA in the ATRX-ZF lines. This is interestingbecause although introduction of ATRX-ZF into the fwa mutant backgrounddid not induce robust methylation at the targeted FWA locus in T2plants, these ATRX-ZF T2 plants nonetheless exhibit early flowering inan otherwise late-flowering fwa mutant background. Regardless of themechanism, the early flowering phenotypes observed in transgenic fwa-4plants housing ATRX-ZF is evidence that FWA was silenced, even if thatsilencing is not a function of re-establishment of DNA methylation atthe FWA promoter.

MOM1-ZF

Flowering time was also analyzed in MOM1-ZF lines. As can be seen inFIG. 16B, four independent T2 lines housing MOM1-ZF showed earlyflowering as compared to the fwa mutant. The results suggest that MOM1was able to be targeted to the FWA locus via ZF-targeting and inducesilencing of this locus.

In order to analyze whether the early flowering phenotype in the MOM1-ZFlines was due to the methylation of the FWA promoter, a bisulfitesequencing assay was performed in independent MOM1-ZF lines that showedthe early flowering phenotype relative to fwa-4. The results, which arepresented in FIG. 17, show that robust DNA methylation wasre-established at FWA in the MOM1-ZF lines. Thus, MOM1-ZF was effectivein targeting methylation at the FWA promoter. Of particular note,MOM1-ZF T2 plant #M2-2 did not contain the MOM1-ZF transgene, yet stillexhibited early flowering and methylation at the FWA promoter. Thisresult suggests that MOM1-ZF-mediated methylation is stably inherited inprogeny plants even after crossing away the MOM1-ZF transgene.

Example 8: DNA-Binding Domain-Targeting of SssI Methyltransferase to theFWA Locus

This Example demonstrates the targeting of SssI methyltransferaseprotein to specific loci to cause CG-specific DNA methylation.

Materials and Methods

Plasmid Construction

For this purpose, a modified pMDC123 plasmid (Curtis et al, 2003, PlantPhys) was created first, containing 1990 bp of the promoter region ofArabidopis UBQ10 gene upstream of the BLRP_ZF108_3×Flag cassette presentin one of the modified pCR2 plasmids described above. Both the UBQ10promoter and BLRP_ZF108_3×Flag are upstream of the gateway cassette(Invitrogen) present in the original pMDC123 plasmid. A plantcodon-optimized cDNA sequence of the Methyltransferase gene fromSpiroplasma sp. strain MQ1 (M.SssI) was cloned first into pENTR/Dplasmid (Invitrogen) and then delivered into the modified pMDC123 by LRreaction (Invitrogen), creating an in-frame fusion of M.SssI cDNA withthe upstream BLRP_ZF_3×Flag cassette.

The nucleotide sequence of the pUBQ10::ZF_3×Flag_M.SssI expressioncassette is presented in SEQ ID NO: 756. Features of this cassetteinclude:UBQ10 promoter (SEQ ID NO: 757), ZF108 (SEQ ID NO: 758), 3×FLAG(SEQ ID NO: 759), plant codon optimized M.SssI (SEQ ID NO: 760), and OCSterm (SEQ ID NO: 761). The amino acid sequence of ZF_3×Flag_SssI ispresented in SEQ ID NO: 762. Features include ZF108 (SEQ ID NO: 763),3×FLAG (SEQ ID NO: 764), and SssI (SEQ ID NO: 765).

Plant Transformation and Flowering Time Measurement

This construct above was introduced into fwa-4 plants usingAgrobacterium-mediated transformation. Transformed lines were selectedusing BASTA. Flowering time was scored by counting the number ofrossette and caulinar leaves.

Bisulfite Sequencing and Data Analysis

BS-Seq libraries were generated using the Ovation Ultralow Methyl-seqLibrary kit from Nugen, and all libraries were sequenced using HiSeqsequencers following manufacturer instructions (Illumina) at a length of50 bp. Bisulfite-Seq (BS-Seq) reads were aligned to the TAIR10 versionof the Arabidopsis thaliana reference genome using BS-seeker. For BS-Sequp to 2 mismatches were allowed and only uniquely mapped reads wereused.

Results

From Example 1, it was found that a ZF-SssI fusion protein in the fwa-4mutant background was able to induce early flowering of these plants ascompared to fwa-4 controls, consistent with silencing of FWA in theZF-SssI lines. These results are presented in graphical form in FIG. 18.

To analyze the methylation status of the FWA promoter in the ZF-SssIlines, a whole-genome bisulfite sequencing assay was performed in twoindependent ZF108-SssI lines that showed the early flowering phenotype.The results, which are presented in FIG. 19 and FIG. 20, demonstratethat the FWA promoter is being methylated in these lines, predominantlyin the CG context. Strikingly, CG methylation in these lines extendedover a much larger region than just the FWA promoter, and in factcovered the entire genome. It thus appears that ZF-SssI is able toinduce genome-wide CG hypermethylation.

As a consequence of the massive accumulation of CG methylationthroughout the genome, plants in the T2 generation showed abnormalphenotypes and pigmentation chimeras in the leaves (FIG. 21A and FIG.21B), probably as a consequence of gene mis-regulation caused byhypermethylation.

Targeting SssI polypeptides to specific loci in a manner that actuallyinduces genome-wide hypermethylation, as described herein, may haveapplications in crop science. For example, this technology may be usedto create novel epigenetic traits, and/or to restore the loss ofmethylation at specific but unknown genes, for instance those that losemethylation during tissue culturing.

Example 9: Targeting of DRM2-MTase to Specific Loci Using SunTag System

This Example demonstrates the targeting of the catalytic domain of DRM2,using a SunTag system, to specific loci in plants and the subsequentinduction of methylation of the targeted loci.

Materials and Methods

Plasmid Construction

The SunTag VP64 constructs as described in Tanenbaum et al, 2014 wereordered from Addgene (pHRdSV40-dCas9-10×GCN4_v4-P2A-BFP andpHRdSV40-scFv-GCN4-sfGFP-VP64-GB1-NLS). These constructs were used asstarting materials to construct a SunTag targeting system usingDRM2-MTase, with all components of the system present on a singlevector. The catalytic methylatransferase domain (residues 255-608) ofthe Nicotiana tabacum DRM2 protein (DRM2-MTase) was used to replace VP64with a methylation effector.

Plant-specific promoters and transcriptional terminators were used inthe new construct, although a human codon-optimized, nuclease-deficient(hdCAS9) was also used. Human codon optimized dCas9 expression, which isfused to one HA tag, two nuclear localization signals, and a linkerfollowed by a 10× epitope tail (10×GCN4), was driven by the plantUBIQUITIN10 (UBQ10) promoter, which is ubiquitously expressed inArabidopsis. The UBQ10 promoter preceding dCas9-10×GCN4 was followed byan Omega translational enhancer sequence. The single chain antibody(scFV) portion of the system, which was also driven by the UBQ10promoter, was fused to superfolder GFP, followed by a linker,DRM2-MTase, another linker, an NLS that was added for plant nuclearlocalization, GB1, and a REX NLS. The dCas9-10×GCN4 and scFv-VP64cassettes were separated by a plant-specific TBS insulator sequence (SEQID NO: 766). gRNA expression was controlled by the Pol III specific U6promoter and termination was controlled by the Pol III terminationsequence.

All features of the constructed SunTag DRM2-MTase system were present ona single vector. The dCAS9-10×GCN4 cassette, scFv-DRM2-MTase cassette,and respective gRNA cassette were cloned into a binary vector usingIn-Fusion cloning. Only one respective gRNA cassette was present in theSunTag vector transformed into plants. A schematic of the expressioncassettes for the SunTag DRM2-MTase system is presented in FIG. 22.

Construction of dCAS9-10×GCN4 Cassette

The dCAS9-10×GCN4 portion of the SunTag DRM2-MTase vector that wasconstructed is contained in expression cassette pUBQ10_OmegaRBC_dCas9_1×HA_2×NLS_flexible linker_10×GCN4 (nucleic acid sequencepresented in SEQ ID NO: 767). This cassette contains the followingfeatures and nucleic acid sequences are provided: UBQ10 promoter (SEQ IDNO: 768), Omega RBC translation enhancer (SEQ ID NO: 769), dCas9 (SEQ IDNO: 770), 1×HA (SEQ ID NO: 771), 2×NLS (SEQ ID NO: 772), flexible linker(SEQ ID NO: 773), 10×GCN4 (SEQ ID NO: 774). The expression cassettefurther included an OCS terminator (SEQ ID NO: 775).

This expression cassette produces a recombinant dCas9-10×GCN4 fusionprotein (SEQ ID NO: 776): dCAS9-1×HA-2×NLS-flexible linker-10×GCN4. Theamino acid sequences of features present in the recombinant fusionprotein expressed from this expression cassette are: dCAS9 (SEQ ID NO:777), 1×HA (SEQ ID NO: 778), 2×NLS (SEQ ID NO: 779), flexible linker(SEQ ID NO: 780), and 10×GCN4 (SEQ ID NO: 781).

Construction of scFv-DRM2-MTase Cassette

The scFv-DRM2-MTase portion of the SunTag DRM2-MTase vector that wasconstructed is contained in expression cassettepUBQ10-scFv-sfGFP-glycine linker-DRM2-MTase-glycine linker-SV40 typeNLS-GB1-REX NLS-NOS terminator (nucleic acid sequence presented in SEQID NO: 782). This cassette contains the following features and nucleicacid sequences are provided: UBQ10 promoter (SEQ ID NO: 783), scFvsingle chain antibody (SEQ ID NO: 784), sfGFP (SEQ ID NO: 785), glycinelinker (SEQ ID NO: 786), DRM2-MTase (SEQ ID NO: 787), glycine linker(SEQ ID NO: 786), SV40 type NLS (SEQ ID NO: 788), GB1 (SEQ ID NO: 789),REX NLS (SEQ ID NO: 790), and NOS terminator (SEQ ID NO: 791).

This expression cassette produces a recombinant scFv-DRM2-MTase fusionprotein (SEQ ID NO: 792): scFv-sfGFP-glycine linker-DRM2-MTase-glycinelinker-SV40 type NLS-GB 1-REX NLS. The amino acid sequences of featurespresent in the recombinant fusion protein expressed from this expressioncassette are: scFv (SEQ ID NO: 793), sfGFP (SEQ ID NO: 794), glycinelinker (SEQ ID NO: 795), DRM2-MTase (SEQ ID NO: 796), SV40-type NLS (SEQID NO: 797), GB1 (SEQ ID NO: 798), and REX NLS (SEQ ID NO: 799).

Construction of gRNA Cassettes

For targeting the FWA gene promoter, a gRNA expression cassette wasconstructed. This expression cassette was U6:gRNA4 (nucleic acidsequence presented in SEQ ID NO: 800). This cassette contains thefollowing features and nucleic acid sequences are provided: U6 promoter(SEQ ID NO: 801), protospacer #4 (SEQ ID NO: 802), gRNA backbone (SEQ IDNO: 803), and PolIII terminator (SEQ ID NO: 804).

Design of tRNA:gRNA Cassette for Targeting the FWA Promoter

A tRNA:gRNA.expression cassette was designed for targeting the FWApromoter. This cassette for targeting FWA includes two different gRNAmolecules and uses protospacer #4 and protospacer #17. The sequence ofthis cassette is presented in SEQ ID NO: 805.

Construct Transformation into Arabidopsis

The vector described above housing the SunTag DRM2-MTase expressionsystem was transformed into Agrobacterium. The vector was thenintroduced into fwa-4 epimutant Arabidopsis thaliana plants usingAgrobacterium-mediated transformation via the floral dip method. T1transgenic plants were selected based on their resistance to Hygromycin.

Fluorescent Microscopy

Visualization of sfGFP fluorescence was performed using a Zeiss confocalmicroscope and recommended wavelengths to visualize GFP fluorescence.Leaf sections were taken from transgenic SunTag DRM2-MTase plants andplaced on microscope slides for visualization.

Bisulfite Sequencing

BS-Seq libraries were generated as previously reported (Cokus et al.,2008) and all libraries were sequenced using the HiSeq 2000 platformfollowing manufacturer instructions (Illumina) at a length of 50 bp.Bisulfite-Seq (BS-Seq) reads were aligned to the TAIR10 version of theArabidopsis thaliana reference genome using BS-seeker. For BS-Seq, up to2 mismatches were allowed and only uniquely mapped reads were used.

Chromatin Immunoprecipitation (ChIP) and ChIP-Seq

Transgenic SunTag DRM2-MTase seeds were plated on MS media and grown.Tissue was collected and two grams were used to grind the tissue.Nuclear Isolation Buffer, protease inhibitors, and 1% formaldehyde wasthen added to the powder. This solution was incubated at roomtemperature on a rotator for 10 minutes. Glycine was then added to stopcross-linking. The solution was filtered, spun down, and the resultingpellet was resuspended with extraction buffer 2+inhibitors. This wasspun down, and the resulting pellet was resuspended with extractionbuffer 3+inhibitors. This was spun and resuspended with Nuclear LysisBuffer. The solution was moved to a new tube and diluted with ChIPdilution buffer. Samples were then sonicated (30 seconds on, 30 secondsoff at maximum power for 15 minutes). dCas9 and the SunTag system werethen immunoprecipitated using an anti-HA antibody. Samples were thenwashed and eluted. DNA was then extracted using phenol-chloroform andlibraries were then made for sequencing by following the proceduresrecommended by the NuGEN kit used. Sequencing reads were then alignedusing bowtie2.

Results

In preliminary work, it was found that the scFv-sfGFP fusion proteinfrom the construct described in Tanenbaum et al, 2014 did not localizeto the nucleus in plants. This construct from Tanenbaum et al, 2014 wasthus re-designed to replace the failed NLS with a linker followed by amodified SV40-type NLS. This is the vector described above in theMaterials and Methods. T2 plants housing this SunTag DRM2-MTase vectorwere similarly evaluated for nuclear localization of thescFv-sfGFP-DRM2-MTase fusion protein. As can be seen in FIG. 23, theSV40-type NLS was able to facilitate nuclear localization of thescFv-sfGFP-DRM2-MTase fusion protein.

Targeting FWA Expression Using gRNA4

Following confirmation that the SunTag DRM2-MTase expression systemcomponents were being expressed and localized to the nucleus asdescribed above, various plant lines were evaluated for whether thissystem could target DRM2-MTase to the FWA promoter and inducemethylation. Various T2 lines housing the SunTag DRM2-MTase constructthat contains gRNA4 (which targets the FWA promoter) were evaluated formethylation levels at the FWA promoter.

Multiple plants from multiple independent T2 SunTag DRM2-MTase+gRNA4lines exhibited increased CG, CHG, and CHH methylation at the FWApromoter as compared to fwa-4 controls. FIG. 24 shows examples of theincreased CHH methylation. In fwa mutants, an epimutation results inloss of methylation from the FWA promoter, as was observed in FIG. 24.The data indicates that introduction of the SunTag DRM2-MTase+gRNA4system was able to induce methylation of the FWA promoter in anotherwise fwa-4 epimutant background.

As described above, the results suggest that, in the SunTag DRM2-MTaselines containing a gRNA that targets the FWA promoter, the gRNA is ableto successfully guide Cas9 to the FWA locus, and that DRM2-MTase is thenable to induce methylation of FWA. To confirm that Cas9 was targeted tothe FWA promoter in the SunTag lines, ChIP-seq of Cas9 using an anti-HAantibody (Cas9 is 1×HA tagged) was performed. As can be seen in FIG. 24,ChIP-seq data confirmed Cas9 binding to FWA via gRNA4.

ChIP-seq samples were further analyzed to view genome-wide binding ofCas9 to genomic regions. The results illustrated in FIG. 24 demonstratean enrichment of Cas9 over the FWA promoter. ChIP-seq analysis alsorevealed only one major off-target of gRNA4 (FIG. 25). This off-targetcontained a PAM sequence+14 base pairs that were complementary to gRNA4.As can be seen in FIG. 25, this off-target in the SunTagDRM2-MTase+gRNA4 lines was also hypermethylated (mostly in the CHHcontext) as compared to an fwa-4 control.

Overall, the results suggest that, in the SunTag DRM2-MTase linescontaining a gRNA that targets the FWA promoter (gRNA4), the gRNA isable to successfully guide Cas9 to the FWA locus, and that DRM2-MTase isthen able to induce methylation of FWA.

Example 10: Additional Zinc Finger Proteins (ZFPs) Fused to DRM2-MTase

This Example describes the use of additional Zinc Finger Proteins (ZFPs)fused to the NtDRM2 methyltransferase domain to methylate the promoterregion of the Arabidopsis SUPERMAN gene.

Materials and Methods

Different artificial Zinc Finger Proteins (ZFPs) were designed asdescribed in Segal et al. 2003; Kolb et al. 2005, and Johnson et al.2014 to bind to the promoter of Arabidopsis SUPERMAN. The resultingsequences were plant-codon optimized and synthesized (IDT technologies).The new ZFPs were cloned in a modified pMDC123 plasmid, between theUBQ10 promoter and a cassette containing 3×Flag, followed by the NtDRM2Methyltransferase domain (DRM2-MTase). The resulting construct wastransformed in agrobacterium and wild type Col0 Arabidopsis plants weretransformed by the floral dip method.

One of the ZFP expression cassettes is calledpMDC_UBQ10::SUP-ZF1_3×Flag_DRM2_MTase. This cassette contains a UBQ10promoter, SUP1-ZF1, 3×FLAG, and DRM2-MTase. The sequence of thiscassette is presented in SEQ ID NO: 843. The amino acid sequence of thefusion protein encoded by this cassette (SUP-ZF1_DRM2-MTase) ispresented in SEQ ID NO: 844. The amino acid sequence of SUP-ZF1 ispresented in SEQ ID NO: 845. The fusion protein includes an N-terminalSUP-ZF1, intervening 3×FLAG, and DRM2-MTase (C-terminal).

Another of the ZFP expression cassettes is calledpMDC_UBQ10::SUP-ZF3_3×Flag_DRM2-MTase. This cassette contains a UBQ10promoter, SUP1-ZF3, 3×FLAG, and DRM2-MTase. The sequence of thiscassette is presented in SEQ ID NO: 846. The amino acid sequence of thefusion protein encoded by this cassette (SUP-ZF3_DRM2-MTase) ispresented in SEQ ID NO: 847. The amino acid sequence of SUP-ZF3 ispresented in SEQ ID NO: 848. The fusion protein includes an N-terminalSUP-ZF3, intervening 3×FLAG, and DRM2-MTase (C-terminal).

Results

DNA methylation of 10 individual transgenic T1 plants was analyzed byMcrBC PCR.

DNA was extracted using a CTAB-based method and digested using the DNAmethylation sensitive restriction enzyme McrBC that specifically digestsmethylated DNA. Digested and undigested DNA was amplified by real-timeqPCRs using oligos designed to amplify the ZFP targeted regions. A lowDigested/Non-digested ratio indicates the presence of methylation at thetargeted loci. A control region that is not targeted by the ZFP was usedas a negative control. The results indicate methylation at the targetregion using both SUP-ZF1 and SUP-ZF3 when either is individually fusedto DRM2-Mtase (FIG. 26).

The presence of methylation at the SUPERMAN gene was also confirmedusing whole genome bisulfite sequencing. DNA from leaves of thedifferent lines expressing the respective ZFP fused to NtDRM2-MTase wasextracted by a CTAB-method. Libraries for whole genome bisulfitesequencing were prepared using the Ovation Ultralow methyl-seq kit(Nugen) and sequenced using the HiSeq 2000 platform followingmanufacturer instructions (Illumina) at a length of 50 bp. Bisulfite-Seq(BS-Seq) reads were aligned to the TAIR10 version of the Arabidopsisthaliana reference genome using BS-seeker. For BS-Seq up to 2 mismatcheswere allowed and only uniquely mapped reads were used. The resultsindicate methylation at the target region using both SUP-ZF1 and SUP-ZF3when either is individually fused to DRM2-Mtase (FIG. 27).

Example 11: DNA Methylation Targeting at FWA with Various Factors

This Example describes additional data showing DNA methylation targetingat FWA with various factors.

Materials, Methods, and Results

DNA from leaves of the different lines expressing ZF108 fused to variousfactors was extracted by a CTAB-method. Libraries for whole genomebisulfite sequencing were prepared using the Ovation Ultralow methyl-sekit (Nugen) and sequenced using the HiSeq 2000 platform followingmanufacturer instructions (Illumina) at a length of 50 bp. Bisulfite-Seq(BS-Seq) reads were aligned to the TAIR10 version of the Arabidopsisthaliana reference genome using BS-seeker. For BS-Seq up to 2 mismatcheswere allowed and only uniquely mapped reads were used.

Results are presented in FIG. 28. The results demonstrate that a numberof proteins, including NRPD1, RDR2, MORC1, RDM1, DMS3, NRPD2,DRM2-MTase, and SssI, when fused to the ZF108 zinc finger, were able totarget methylation at the FWA promoter. ZF108 chromatinimmunoprecipitation demonstrates that ZF108 was bound at the targetedregion of the FWA locus.

Example 12: Off-Targets of ZF108

This Example illustrates additional regions of the Arabidopsis genometargeted by the ZF108 artificial zinc finger.

Materials and Methods

DNA from leaves of different lines expressing ZF108 fused to variousfactors was extracted by a CTAB-method. Libraries for whole genomebisulfite sequencing were prepared using the Ovation Ultralow methyl-seqkit (Nugen) and sequenced using the HiSeq 2000 platform followingmanufacturer instructions (Illumina) at a length of 50 bp. Bisulfite-Seq(BS-Seq) reads were aligned to the TAIR10 version of the Arabidopsisthaliana reference genome using BS-seeker. For BS-Seq up to 2 mismatcheswere allowed and only uniquely mapped reads were used.

Results

The results demonstrate DNA methylation targeting at a second locationin the Arabidopsis genome with two sequences very similar to the ZF108target locus. Both Col0 and fwa-4 plants have very little pre-existingmethylation at this site, but the ZF108 fusion protein containing plantscontain methylation in all three sequence contexts (FIG. 29). A ChIP-seqanalysis of the ZF108 zinc finger fused to either the HA tag or aDMS3-FLAG tag shows enrichment of ZF108 at both FWA and this secondlocation with sequences related to the zinc finger binding site (FIG.30).

Example 13: DNA Methylation-Independent Silencing of Targeted Loci

This Example describes the ability of ZF108 fusions to DMS3, HDA6,JMJ14, SHH2 and SUVR2 to silence FWA and affect flowering time in a DNAmethylation-independent manner.

Materials, Methods, and Results

Plants expressing ZF108 fused to DMS3, HDA6, JMJ14 or SHH2 (described inExample 6) were transformed into either fwa-4 or fwa-4 drm1 drm2 triplemutants, defective in the two de-novo methyltransferases in Arabidopsisand, therefore, incapable of de-novo methylating any sequences.Importantly, plants expressing the different ZF108 fusions in bothmutant backgrounds were able to cause an early flowering phenotype,suggesting that they were able to repress FWA expression and cause earlyflowering, even in the absence of DNA methylation (fwa-4×drm1/2) (FIG.31, FIG. 32, FIG. 33, and FIG. 34).

To further validate that this effect on flowering time was happening inthe absence of DNA methylation, BS—PCR and whole genome bisulfitesequencing were performed as described in previous examples (FIG. 35 andFIG. 36). The results indicate that, indeed, DNA methylation was absentat the FWA promoter in plants expressing the different fusions in bothmutant backgrounds, fwa-4 or fwa-4×drm1/2, confirming that these factorscan cause early flowering in the absence of DNA methylation. TheZF108-SUVR2 plants also showed no DNA methylation at the FWA gene (FIG.36), suggesting that SUVR2 is also capable of causing silencing of FWAin the absence of DNA methylation.

In Example 6 herein, it was found that HDA6, JMJ14, SHH2, and SUVR2 did,in that particular case, cause methylation of FWA. However, aselaborated upon in this Example, it has also been found that thisinduction of methylation by these factors does not always occur. Thus,it appears that these factors can in some cases trigger methylation ofFWA, but in most cases do not. Regardless, the data demonstrate thatthese factors can induce silencing of FWA when targeted to that locus,even in the absence of inducing DNA methylation at that locus.

Example 14: Heritable Silencing Induced by ZF108-SssI

This Example describes the inheritance of DNA methylation and FWAsilencing and early flowering in the absence of the ZF108-SssI transgeneonce it has genetically segregated out.

Materials and Methods

DNA from T2 and T3 ZF+ and ZF− plants was extracted by a CTAB-basedmethod and libraries for whole genome bisulfite sequencing were preparedusing the Ovation Ultralow methyl-seq kit. Libraries were sequencedusing the HiSeq 2000 platform following manufacturer instructions(Illumina) at a length of 50 bp. Bisulfite-Seq (BS-Seq) reads werealigned to the TAIR10 version of the Arabidopsis thaliana referencegenome using BS-seeker. For BS-Seq up to 2 mismatches were allowed andonly uniquely mapping reads were used.

Results

fwa-4 plants were transformed with the ZF108-SssI transgene. T1 plantswere selfed to produce the T2 generation, and individual plants thatstill contained the transgene (ZF+) or had segregated it out (ZF−) wereselected. The T3 progeny of these plants were grown and flowering timewas scored and compared to controls, Col0 and fwa-4. The results showthat DNA methylation triggered by ZF108-SssI, and the accompanyingtransition to early flowering, is maintained even when the transgene issegregated out (FIG. 37, FIG. 38, and FIG. 39). In addition, CGmethylation which had been established by ZF108-SssI at many otherregions of the genome were also maintained after the ZF108-SssItransgene was segregated away.

The ability of SssI to cause CG methylation throughout the genome asdescribed herein may have applications in restoring methylation inplants. For example, plants that undergo the tissue culture processesnormally involved in plant transformation show losses of DNA methylationat hundreds of locations. These losses are heritable, and can causechanges in gene expression (Stroud et al., 2013). It is possible thatZF108-SssI could be used to restore methylation in plants that haveundergone tissue culture.

Example 15: Zinc Finger Targeting of MBD9 to FWA

This Example describes the use of MBD9 fused to ZF108 to repressexpression of the FWA gene.

Materials and Methods

A genomic construct of MBD9, including a 1 Kb promoter region, wascloned into pENTR/D plasmid. Then, a cassette containing 3×Flag andZF108 was cloned downstream of MBD9 and the resulting construct wastransferred into a modified pEG302 binary vector. This construct wastransformed into Agrobacterium and introduced in fwa-4 plants by thefloral dip method.

The nucleic acid sequence of the expression cassette, MBD9_3×Flag_ZF108,is set forth in SEQ ID NO: 849. The amino acid sequence of the fusionprotein encoded by this cassette is set forth in SEQ ID NO: 850.

T1 transgenic plants, together with Col0 and fwa-4 controls, were grownand flowering time was scored by counting the number of total leaves.

Results

ZF108-MBD9 plants displayed an early flowering phenotype in 6 out of 38tested plants (Table 15A). This indicates that MBD9 is able to causesilencing of FWA.

TABLE 15A Flowering Time Results early flowering late flowering MBD9-ZF6 32

In order to determine if the FWA promoter is being methylated in theselines, an McrBC PCR experiment was done using the methylation sensitiverestriction enzyme McrBC. Briefly, genomic DNA from Col0, fwa-4 and 7independent T1 lines expressing MBD9-ZF, 6 of them showing an earlyflowering phenotype, was digested with McrBC for 4 h at 37° C. The sameamount of DNA was mock-digested (no restriction enzyme) under the sameconditions. qPCR using the resulting samples was performed with oligosthat amplify the FWA promoter, or a control region that, similar to FWApromoter, shows methylation in Col0 but not in fwa-4. Then, the ratiobetween digested and undigested samples was calculated. The resultsclearly indicate that the lines expressing MBD9-ZF do not showmethylation at the FWA promoter (FIG. 40). MBD9 is thus able to causesilencing of FWA in the absence of DNA methylation.

Example 16: Targeting of DRM2-MTase to the SUPERMAN Locus Using theSunTag System

This Example demonstrates the targeting of DRM2-MTase to the SUPERMANlocus using the SunTag system and the subsequent establishment of DNAmethylation and silencing.

Materials and Methods

Materials and Methods used in this Example are similar to the Materialsand Methods described in Example 9. One notable difference is that twodifferent U6-driven guide RNAs are used to target SUPERMAN, as opposedto targeting FWA as in Example 9.

For targeting SUPERMAN, two sgRNA expression cassettes were constructedand were present on the same binary vector described in Example 9. Eachcassette was driven by the U6 promoter (SEQ ID NO: 860). The twoprotospacer sequences are presented in SEQ ID NO: 851 and SEQ ID NO:852. The sgRNA backbone sequence is presented in SEQ ID NO: 853.

Results

Following confirmation that the SunTag DRM2-MTase expression systemcomponents were being expressed and localized to the nucleus, variousplant lines were evaluated to assess targeting of DRM2-MTase to SUPERMANand induction of methylation. Various T1 lines housing the SunTagDRM2-MTase construct that contains the two guides (which target thepromoter region of SUPERMAN) were evaluated for methylation levels atSUPERMAN's promoter region.

Multiple plants from multiple independent T1 SunTag DRM2-MTase+sgRNA1/2lines exhibited increased CHH and CHG methylation at SUPERMAN's promoterregion as compared to Col controls. FIG. 42 and FIG. 43 show examples ofthe increased CHH and CHG methylation, respectively. As shown in thefigures, there is no methylation present in the controls, and the SunTagconstruct successfully introduces methylation at the targeted sites.

qRT-PCR was performed to check for repression of SUPERMAN transcripts inflowers of T1 lines as compared to Col controls. As shown in FIG. 44,line 1 showed downregulation of SUPERMAN expression by 2-fold ascompared to the control. Since full gene silencing by DNA methylationoften takes multiple sexual generations, without wishing to be bound bytheory, it is thought that further silencing of SUPERMAN will occur inselfed progeny of these plants.

Overall, the results suggest that SunTag DRM2-MTase lines containing 2guides targeting SUPERMAN are able to successfully guide dCas9 to theSUPERMAN locus, and that DRM2-MTase is then able to induce methylationof SUPERMAN and gene silencing.

Example 17: Targeting of DNMT3A-3L to the FWA Locus Using the SunTagSystem

This Example demonstrates the targeting of the DNMT3A catalytic domainfused to the C-terminal domain of DNMT3L to the FWA locus using theSunTag system and the subsequent establishment of DNA methylation andsilencing. Transforming Arabidopsis fwa epiallele plants with the SunTagconstruct led to methylation of the FWA promoter.

Materials and Methods

Materials and Methods used in this Example are similar to the Materialsand Methods described in Example 9. One notable difference is that theDNMT3A-3L fusion is being used, as opposed to DRM2-MTase as described inExample 9. For targeting FWA, U6 driven sgRNA4 was used as described inExample 9.

The construct in this Example contained a DNMT3A-3L fusion. Thecatalytic methyltransferase domain of the DNMT3A protein and theC-terminal domain of the 3L protein were fused (DNMT3A-3L) and used toreplace VP64 with a methylation effector. dCas9, single chain variablefragment (scFv) antibodies, and guide RNAs (gRNA) were cloned into abinary vector using In-Fusion cloning, which were then used for floraldipping in Arabidopsis thaliana.

The UBQ10 promoter preceding dCas9-GCN4×10 was followed by an Omegatranslational enhancer sequence. dCas9-GCN4×10 andscFv-GCN4-sfGFP-DNMT3A-3L-GB1-NLS cassettes were separated by aplant-specific TBS insulator sequence. gRNA expression was controlled bythe Pol III specific U6 promoter and termination was controlled by thePol III termination sequence.

The dCas9 expression cassette contained UBQ10_OmegaRBC_dCas9_1×HA_NLSNLS_flexible linker_GCN4×10. The nucleotide sequenceof this cassette is presented in SEQ ID NO: 854. The fusion proteinencoded from this nucleotide sequence (dCas9_1×HA_NLSNLS_flexiblelinker_GCN4×10) is presented in SEQ ID NO: 855.

The scFv expression cassette contained UBQ10_scFv_sfGFP_unique BsiWIsite_glycine linker_DNMT3A (catalytic)-DNMT3L (C-terminal)_glycinelinker_NLS_BsiWI site_GB1_REX NLS_NOS terminator. The nucleotidesequence of this cassette is presented in SEQ ID NO: 856. The fusionprotein encoded from this nucleotide sequence (scFv_sfGFP_glycinelinker_DNMT3A (catalytic)-DNMT3L (C-terminal)_glycine linker_NLS_GB1_REXNLS) is presented in SEQ ID NO: 857.

The gRNA was as follows: U6 promoter_protospacer #4_gRNA backbone_PolIII terminator. The nucleotide sequence of this gRNA is presented in SEQID NO: 858.

Results

Following confirmation that the SunTag DNMT3A-3L expression systemcomponents were being expressed and localized to the nucleus asdescribed in Example 9, various plant lines were evaluated for whetherthis system could target DNMT3A-3L to FWA and induce methylation.Various T1 lines housing the SunTag DNMT3A-3L construct that containssgRNA4 (which targets the promoter of FWA) were evaluated formethylation levels at FWA's promoter region.

Multiple plants from multiple independent T1 SunTag DNMT3A-3L+sgRNA4lines exhibited increased CG methylation at FWA's promoter region ascompared to fwa epiallele controls plants. FIG. 45 shows examples of theincreased CG methylation. In fwa-4, an epimutation results in loss ofmethylation from the FWA promoter. As shown in FIG. 45, there is nomethylation present in the control, and the SunTag constructsuccessfully introduces methylation at the targeted site. Two out ofeight lines tested (the same two shown in FIG. 45), also exhibited aslightly early flowering phenotype, indicating partial silencing of FWA.

Overall, the results suggest that SunTag DNMT3A-3L lines containingsgRNA4 targeting FWA are able to successfully guide dCas9 to the FWAlocus, and that DNMT3A-3L is then able to induce methylation of FWA.This methylation targeting was not as efficient as that seen in SunTagDRM2-MTase plants. Without wishing to be bound by theory, it is thoughtthat increasing the number of gRNAs may increase the efficiency ofmethylation targeting by SunTag DNMT3A-3L.

Example 18: Additional Information

Transgenic T2 plants expressing the MS2-DRM2-MTase construct anddifferent gRNAs targeting the FWA promoter (gRNA5, gRNA8 andgRNA3-gRNA14-gRNA17) (described in Example 3) were analyzed forflowering time, together with fwa-4 and Col0 controls. All thetransgenic lines showed late flowering in T1 and T2 suggesting thatthese constructs were ineffective in causing FWA silencing. Methylationlevels of different transgenic lines expressing dCas9 and MS2-MTaseproteins were analyzed by whole genome bisulfite sequencing. Resultsshowed no methylation at the FWA promoter.

T1 and T2 transgenic plants expressing straight fusions of dCas9 to DMS3or DRM2-MTase together with gRNAs targeting the FWA promoter (describedin Example 1), were analyzed for flowering time and DNA methylation bywhole genome bisulfite sequencing. None of the lines showed earlyflowering or DNA methylation at the FWA promoter suggesting that theseconstructs were not effective in causing silencing or DNA methylation.

A fragment containing hdSpdCas9 fused to DNMT3A and DNMT3L was amplifiedfrom the hdSpCas9-3a3-3×Flag plasmid (Albert Jeltsch's lab) and clonedinto a modified pMDC123 plasmid between the Arabidopsis UBQ10 promoterand the NOS terminator. Two gRNAs cassettes, each containing a U6promoter and a gRNA targeting the FWA promoter were cloned in tandemupstream of the UBQ10 promoter. The resulting plasmid was introducedinto agrobacterium and fwa-4 plants were transformed by the floral dipmethod. Transgenic plants were scored for expression of the transgeneand flowering time together with fwa-4 and Col0 controls. All the linesexpressing the transgene were late flowering. Methylation of twoindependent T1 plants expressing the transgene was analyzed bywhole-genome bisulfite sequencing. Results showed no methylation at FWApromoter. These results suggest that these constructs were ineffectivein triggering silencing and methylation of FWA.

A CG-specific methyltransferase from Mycoplasma penetrans (MpeI) wasplant-codon optimized and gene synthesized (IDT technologies). Theresulting fragment was cloned into a modified pMDC123 plasmid downstreamof a cassette containing UBQ10 promoter, ZF108 and 3×Flag. The resultingplasmid was transformed into Agrobacterium and introduced into fwa-4plants by the floral dip method. 47 transgenic T1 plants were analyzedfor flowering time and all showed a late flowering phenotype, indicatingthat this construct was not effective in inducing gene silencing.

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What is claimed is:
 1. A method for reducing expression of one or moretarget nucleic acids in a plant, comprising: (a) providing a plantcomprising: a recombinant nucleic acid encoding a recombinantpolypeptide comprising a nuclease-deficient CAS9 polypeptide (dCAS9) orfragment thereof and a polypeptide selected from the group consisting ofan SHH1 polypeptide or fragment thereof, an SHH2 polypeptide or fragmentthereof, an AGO4 polypeptide or fragment thereof, an HDA6 polypeptide orfragment thereof, an NRPD1 polypeptide or fragment thereof, a JMJ14polypeptide or fragment thereof, an RDR2 polypeptide or fragmentthereof, an NRPD2A/NRPE2 polypeptide or fragment thereof, anNRPB3/NRPD3/NRPE3A polypeptide or fragment thereof, an NRPE3Bpolypeptide or fragment thereof, an NRPB11/NRPD11/NRPE11 polypeptide orfragment thereof, an NRPB10/NRPD10/NRPE10 polypeptide or fragmentthereof, an NRPB12/NRPD12/NRPE12 polypeptide or fragment thereof, anNRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof; and a crRNA and a tracrRNA, orfusions thereof; (b) growing the plant under conditions whereby therecombinant nucleic acid is expressed and whereby the recombinantpolypeptide is targeted to the one or more target nucleic acids, therebyreducing expression of the one or more target nucleic acids.
 2. Themethod of claim 1, wherein the recombinant polypeptide interacts with anRNA polymerase.
 3. The method of claim 2, wherein the RNA polymerase isRNA polymerase IV or RNA polymerase V.
 4. The method of any one ofclaims 1-3, wherein the recombinant polypeptide induces RNA-directed DNAmethylation.
 5. The method of any one of claims 1-4, wherein the one ormore target nucleic acids are endogenous nucleic acids.
 6. The method ofany one of claims 1-4, wherein the one or more target nucleic acids areheterologous nucleic acids.
 7. The method of any one of claims 1-6,wherein expression of the one or more target nucleic acids is silenced.8. A recombinant nucleic acid which encodes a recombinant polypeptidecomprising a nuclease-deficient CAS9 polypeptide (dCAS9) and apolypeptide selected from the group consisting of an SHH1 polypeptide orfragment thereof, an SHH2 polypeptide or fragment thereof, an AGO4polypeptide or fragment thereof, an HDA6 polypeptide or fragmentthereof, an NRPD1 polypeptide or fragment thereof, a JMJ14 polypeptideor fragment thereof, an RDR2 polypeptide or fragment thereof, anNRPD2A/NRPE2 polypeptide or fragment thereof, an NRPB3/NRPD3/NRPE3Apolypeptide or fragment thereof, an NRPE3B polypeptide or fragmentthereof, an NRPB11/NRPD11/NRPE11 polypeptide or fragment thereof, anNRPB10/NRPD10/NRPE10 polypeptide or fragment thereof, anNRPB12/NRPD12/NRPE12 polypeptide or fragment thereof, anNRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof.
 9. An expression vector comprisingthe recombinant nucleic acid of claim
 8. 10. A host cell comprising theexpression vector of claim
 9. 11. A recombinant plant comprising therecombinant nucleic acid of claim
 9. 12. A plant having reducedexpression of one or more target nucleic acids as a consequence of themethod of any one of claims 1-7.
 13. A progeny plant of the plant ofclaim
 12. 14. The progeny plant of claim 13, wherein the progeny planthas reduced expression of the one or more target nucleic acids and doesnot comprise the recombinant nucleic acid.
 15. A method for reducingexpression of one or more target nucleic acids in a plant, comprising:(a) providing a plant comprising: a recombinant nucleic acid encoding arecombinant polypeptide selected from the group consisting of anSHH1-like protein, an SHH2-like protein, an AGO4-like protein, anHDA6-like protein, an NRPD1-like protein, a JMJ14-like protein, anRDR2-like protein, an NRPD2A/NRPE2-like protein, anNRPB3/NRPD3/NRPE3A-like protein, an NRPE3B-like protein, anNRPB11/NRPD11/NRPE11-like protein, an NRPB10/NRPD10/NRPE10-like protein,an NRPB2/NRPD12/NRPE12-like protein, an NRPB6A/NRPD6A/NRPE6A-likeprotein, an NRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-likeprotein, an NRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein; and a crRNA and a tracrRNA, or fusions thereof;and wherein the plant expresses a dCAS9 protein, (b) growing the plantunder conditions whereby the recombinant nucleic acid is expressed andwhereby the recombinant polypeptide is targeted to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids.
 16. The method of claim 15, wherein therecombinant polypeptide comprises a dCAS9 protein or fragment thereof.17. The method of claim 15, wherein the recombinant polypeptidecomprises an MS2 coat protein or fragment thereof.
 18. The method ofclaim 15, wherein the recombinant polypeptide comprises an scFV antibodyor fragment thereof.
 19. The method of any one of claims 15-18, whereinthe recombinant polypeptide interacts with an RNA polymerase.
 20. Themethod of claim 19, wherein the RNA polymerase is RNA polymerase IV orRNA polymerase V.
 21. The method of any one of claims 15-20, wherein therecombinant polypeptide induces RNA-directed DNA methylation.
 22. Themethod of any one of claims 15-21, wherein the one or more targetnucleic acids are endogenous nucleic acids.
 23. The method of any one ofclaims 15-21, wherein the one or more target nucleic acids areheterologous nucleic acids.
 24. The method of any one of claims 15-23,wherein expression of the one or more target nucleic acids is silenced.25. A recombinant nucleic acid which encodes a recombinant polypeptideselected from the group consisting of an SHH1-like protein, an SHH2-likeprotein, an AGO4-like protein, an HDA6-like protein, an NRPD1-likeprotein, a JMJ14-like protein, an NRPD2A/NRPE2-like protein, anNRPB3/NRPD3/NRPE3A-like protein, an NRPE3B-like protein, anNRPB11/NRPD11/NRPE11-like protein, an NRPB10/NRPD10/NRPE10-like protein,an NRPB12/NRPD12/NRPE12-like protein, an NRPB6A/NRPD6A/NRPE6A-likeprotein, an NRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-likeprotein, an NRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein.
 26. An expression vector comprising therecombinant nucleic acid of claim
 25. 27. A host cell comprising theexpression vector of claim
 26. 28. A recombinant plant comprising therecombinant nucleic acid of claim
 25. 29. A plant having reducedexpression of one or more target nucleic acids as a consequence of themethod of any one of claims 15-24.
 30. A progeny plant of the plant ofclaim
 29. 31. The progeny plant of claim 30, wherein the progeny planthas reduced expression of the one or more target nucleic acids and doesnot comprise the recombinant nucleic acid.
 32. A method for reducingexpression of one or more target nucleic acids in a plant, comprising:(a) providing a plant comprising a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide comprising afirst amino acid sequence comprising a DNA-binding domain and a secondamino acid sequence comprising a polypeptide selected from the groupconsisting of an SHH1 polypeptide or fragment thereof, an SHH2polypeptide or fragment thereof, an AGO4 polypeptide or fragmentthereof, an HDA6 polypeptide or fragment thereof, an NRPD1 polypeptideor fragment thereof, a JMJ14 polypeptide or fragment thereof, an RDR2polypeptide or fragment thereof, an NRPD2A/NRPE2 polypeptide or fragmentthereof, an NRPB3/NRPD3/NRPE3A polypeptide or fragment thereof, anNRPE3B polypeptide or fragment thereof, an NRPB11/NRPD11/NRPE11polypeptide or fragment thereof, an NRPB10/NRPD10/NRPE10 polypeptide orfragment thereof, an NRPB12/NRPD12/NRPE12 polypeptide or fragmentthereof, an NRPB6A/NRPD6A/NRPE6A polypeptide or fragment thereof, anNRPB6B/NRPD6B/NRPE6B polypeptide or fragment thereof, an NRPB8A/NRPE8Apolypeptide or fragment thereof, an NRPB8B/NRPD8B/NRPE8B polypeptide orfragment thereof, an NRPE5 polypeptide or fragment thereof, anNRPD4/NRPE4 polypeptide or fragment thereof, an NRPE7 polypeptide orfragment thereof, an NRPD7 polypeptide or fragment thereof, anNRPB5/NRPD5 polypeptide or fragment thereof, an NRPB9A/NRPD9A/NRPE9Apolypeptide or fragment thereof, an NRPB9B/NRPD9B/NRPE9B polypeptide orfragment thereof, an ATRX polypeptide or fragment thereof, a MOM1polypeptide or fragment thereof, a MORC1 polypeptide or fragmentthereof, an SssI polypeptide or fragment thereof, a DRM2-MTasepolypeptide or fragment thereof, a DNMT3A polypeptide or fragmentthereof, a DNMT3L polypeptide or fragment thereof, an MBD9 polypeptideor fragment thereof, a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof; and (b) growing the plant underconditions whereby the recombinant polypeptide encoded by therecombinant nucleic acid is expressed and binds to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids.
 33. The method of claim 32, wherein theDNA-binding domain comprises a zinc finger domain.
 34. The method ofclaim 33, wherein the zinc finger domain comprises two, three, four,five, six, seven, eight, or nine zinc fingers.
 35. The method of claim33, wherein the zinc finger domain is a zinc finger array.
 36. Themethod of claim 33, wherein the zinc finger domain is selected from thegroup consisting of a Cys2His2 (C2H2) zinc finger domain, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, and a zinc binuclearcluster domain.
 37. The method of claim 32, wherein the DNA-bindingdomain is selected from the group consisting of a TAL effector targetingdomain, a helix-turn-helix family DNA-binding domain, a basic domain, aribbon-helix-helix domain, a TBP domain, a barrel dimer domain, a realhomology domain, a BAH domain, a SANT domain, a Chromodomain, a Tudordomain, a Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.38. The method of claim 32, wherein the DNA-binding domain comprises aTAL effector targeting domain.
 39. The method of claim 32, wherein theDNA-binding domain comprises three C2H2 zinc finger domains.
 40. Themethod of claim 32, wherein the recombinant polypeptide interacts withan RNA polymerase.
 41. The method of claim 40, wherein the RNApolymerase is RNA polymerase IV or RNA polymerase V.
 42. The method ofany one of claims 32-41, wherein the recombinant polypeptide inducesRNA-directed DNA methylation.
 43. The method of any one of claim 32-42,wherein the one or more target nucleic acids are endogenous nucleicacids.
 44. The method of any one of claim 32-42, wherein the one or moretarget nucleic acids are heterologous nucleic acids.
 45. The method ofany one of claim 32-42, wherein expression of the one or more targetnucleic acids is silenced.
 46. A method for reducing expression of oneor more target nucleic acids in a plant, comprising: (a) providing aplant comprising a recombinant polypeptide selected from the groupconsisting of an SHH1-like protein, an SHH2-like protein, an AGO4-likeprotein, an HDA6-like protein, an NRPD1-like protein, a JMJ14-likeprotein, an RDR2-like protein, an NRPD2A/NRPE2-like protein, anNRPB3/NRPD3/NRPE3A-like protein, an NRPE3B-like protein, anNRPB11/NRPD11/NRPE11-like protein, an NRPB10/NRPD10/NRPE10-like protein,an NRPB12/NRPD12/NRPE12-like protein, an NRPB6A/NRPD6A/NRPE6A-likeprotein, an NRPB6B/NRPD6B/NRPE6B-like protein, an NRPB8A/NRPE8A-likeprotein, an NRPB8B/NRPD8B/NRPE8B-like protein, an NRPE5-like protein, anNRPD4/NRPE4-like protein, an NRPE7-like protein, an NRPD7-like protein,an NRPB5/NRPD5-like protein, an NRPB9A/NRPD9A/NRPE9A-like protein, anNRPB9B/NRPD9B/NRPE9B-like protein, an ATRX-like protein, a MOM1-likeprotein, a MORC1-like protein, an SssI-like protein, a DRM2-MTase-likeprotein, a DNMT3A-like protein, a DNMT3L-like protein, a MBD9-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and an FRG-like protein; and (b) growing the plant under conditionswhereby the recombinant polypeptide is targeted to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids.
 47. A method for reducing expression of one ormore target nucleic acids in a plant, comprising: (a) providing a plantcomprising: a first recombinant polypeptide comprising anuclease-deficient CAS9 polypeptide (dCAS9) or fragment thereof and amultimerized epitope; a second recombinant polypeptide comprising aDRM2-MTase polypeptide or a DNMT3A-DNMT3L fusion polypeptide, and anaffinity polypeptide that specifically binds to the epitope; a crRNA anda tracrRNA, or fusions thereof; and (b) growing the plant underconditions whereby the first and second recombinant polypeptides aretargeted to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids.
 48. A recombinantvector comprising: a first nucleic acid sequence comprising a plantpromoter and that encodes a recombinant polypeptide comprising anuclease-deficient CAS9 polypeptide (dCAS9) or fragment thereof and amultimerized epitope; a second nucleic acid sequence comprising a plantpromoter and that encodes a recombinant polypeptide comprising aDRM2-MTase polypeptide or a DNMT3A-DNMT3L fusion polypeptide, and anaffinity polypeptide that specifically binds to the epitope; and a thirdnucleic acid sequence comprising a promoter and that encodes a crRNA anda tracrRNA, or fusions thereof.
 49. A host cell comprising the vector ofclaim
 48. 50. A recombinant plant comprising the vector of claim
 48. 51.A plant having reduced expression of one or more target nucleic acids asa consequence of the method of claim 46 or claim
 47. 52. A progeny plantof the plant of claim
 51. 53. The progeny plant of claim 52, wherein theprogeny plant has reduced expression of the one or more target nucleicacids and does not comprise the recombinant polypeptide targeted to theone or more target nucleic acids.